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Wang SX, Summage-West CV, Kim SG. Complete genome sequence of Parabacteroides distasonis strain GP102, isolated from the cecum of a morbid pregnant laboratory guinea pig ( Cavia porcellus). Microbiol Resour Announc 2024; 13:e0125923. [PMID: 38376195 DOI: 10.1128/mra.01259-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Parabacteroides distasonis is an anaerobic bacterium with ambivalent health effects. P. distasonis strain GP102 was isolated from the cecum content of a morbid pregnant laboratory guinea pig (Cavia porcellus). The genome consists of one circular 5.39-Mbp chromosome with a G + C content of 44.79%.
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Affiliation(s)
- Sharon X Wang
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Christine V Summage-West
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Sung Guk Kim
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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2
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Fernández Vecilla D, Roche Matheus MP, Urrutikoetxea Gutiérrez MJ, Aspichueta Vivanco C, Iglesias Hidalgo G, Pérez Ramos IS, Díaz de Tuesta Del Arco JL. A case report of multiple abscess co-infected with Eggerthella lenta and Desulfovibrio desulfuricans identificated with MALDI-TOF mass spectrometer. Rev Esp Quimioter 2024; 37:106-109. [PMID: 38050695 PMCID: PMC10874660 DOI: 10.37201/req/081.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Basurto University Hospital. Montevideo Avenue, 18, Gurtubay pavilion, 3rd floor. 48013, Bilbao (Basque country). Spain.
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Rosenbaum FP, Müller V. A novel hexameric NADP + -reducing [FeFe] hydrogenase from Moorella thermoacetica. FEBS J 2024; 291:596-608. [PMID: 37885325 DOI: 10.1111/febs.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023]
Abstract
Acetogenic bacteria such as the thermophilic anaerobic model organism Moorella thermoacetica reduce CO2 with H2 as a reductant via the Wood-Ljungdahl pathway (WLP). The enzymes of the WLP of M. thermoacetica require NADH, NADPH, and reduced ferredoxin as reductants. Whereas an electron-bifurcating ferredoxin- and NAD+ -reducing hydrogenase HydABC had been described, the enzyme that reduces NADP+ remained to be identified. A likely candidate is the HydABCDEF hydrogenase from M. thermoacetica. Genes encoding for the HydABCDEF hydrogenase are expressed during growth on glucose and dimethyl sulfoxide (DMSO), an alternative electron acceptor in M. thermoacetica, whereas expression of the genes hydABC encoding for the electron-bifurcating hydrogenase is downregulated. Therefore, we have purified the hydrogenase from cells grown on glucose and DMSO to apparent homogeneity. The enzyme had six subunits encoded by hydABCDEF and contained 58 mol of iron and 1 mol of FMN. The enzyme reduced methyl viologen with H2 as reductant and of the physiological acceptors tested, only NADP+ was reduced. Electron bifurcation with pyridine nucleotides and ferredoxin was not observed. H2 -dependent NADP+ reduction was optimal at pH 8 and 60 °C; the specific activity was 8.5 U·mg-1 and the Km for NADP+ was 0.086 mm. Cell suspensions catalyzed H2 -dependent DMSO reduction, which is in line with the hypothesis that the NADP+ -reducing hydrogenase HydABCDEF is involved in electron transfer from H2 to DMSO.
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Affiliation(s)
- Florian P Rosenbaum
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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Mazel F, Guisan A, Parfrey LW. Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes. Mol Ecol 2024; 33:e16862. [PMID: 36786039 DOI: 10.1111/mec.16862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023]
Abstract
Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Williams TJ, Daboin C, Kim P, Guo F, de Figueiredo P, Alge DL. Enzyme-functionalized alginate microparticles enable anaerobic culture under ambient oxygen. Biotechnol Bioeng 2024; 121:219-227. [PMID: 37807712 DOI: 10.1002/bit.28566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/10/2023]
Abstract
Methods for culturing oxygen-sensitive cells and organisms under anaerobic conditions are vital to biotechnology research. Here, we report a biomaterial-based platform for anaerobic culture that consists of glucose oxidase (GOX) functionalized alginate microparticles (ALG-GOX), which are designed to deplete dissolved [O2 ] through enzymatic activity. ALG-GOX microparticles were synthesized via a water-in-oil emulsion and had a size of 132.0 ± 51.4 µm. Despite having a low storage modulus, the microparticles remained stable under aqueous conditions due to covalent crosslinking through amide bonds. Enzyme activity was tunable based on the loaded GOX concentration, with a maximum activity of 3.6 ± 0.3 units/mg of microparticles being achieved at an initial loading concentration of 5 mg/mL of GOX in alginate precursor solution. High enzyme activity in ALG-GOX microparticles resulted in rapid oxygen depletion, producing a suitable environment for anaerobic culture. Microparticles loaded with both GOX and catalase (ALG-GOX-CAT) to reduce H2 O2 buildup exhibited sustained activity for potential long-term anaerobic culture. ALG-GOX-CAT microparticles were highly effective for the anaerobic culture of Bacteroides thetaiotaomicron, with 10 mg/mL of ALG-GOX-CAT microparticles supporting the same level of growth in an aerobic environment compared to an anaerobic chamber after 16 h (8.70 ± 0.96 and 10.03 ± 1.03 million CFU, respectively; N.S. p = 0.07). These microparticles could be a valuable tool for research and development in biotechnology.
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Affiliation(s)
- Tyrell J Williams
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Claudia Daboin
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul Kim
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Fengguang Guo
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
- Department of Veterinary Pathobiology, School of Veterinary Medicine, Texas A&M University, College Station, Texas, USA
| | - Daniel L Alge
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas, USA
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Fernández Vecilla D, Roche Matheus MP, Calvo Muro FE, Iglesias Hidalgo G, Díaz de Tuesta Del Arco JL. Identification of curved Gram-negative rods by MALDI-TOF mass spectrometer in a patient with Fournier ́s gangrene. A bacteremia caused by Desulfovibrio desulfuricans and Escherichia coli. Rev Esp Quimioter 2023; 36:629-631. [PMID: 37767548 DOI: 10.37201/req/026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Clinical Microbiology and Parasitology. Hospital Universitario de Basurto. Avenida Montevideo nº18, Gurtubay pavilion, 3rd floor. Postal code: 48013, Bilbao (Basque country). Spain.
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Dai J, Li XG, Zhang WJ, Wu LF. Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921840 DOI: 10.1099/ijsem.0.006151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A novel anaerobic heterotrophic bacterium, designated strain SWIR-1T, was isolated from a deep-sea hydrothermal vent field sample collected from the Southwest Indian Ridge at a depth of 2700 m. Phylogenetic analysis indicated that strain SWIR-1T belongs to the genus Tepidibacter, and the most closely related species are Tepidibacter mesophilus B1T (99.1 % 16S rRNA gene sequence similarity), Tepidibacter formicigenes DV1184T (94.6 %) and Tepidibacter thalassicus SC562T (93.9 %). Strain SWIR-1T shares 77.3-87.2 % average nucleotide identity and 21.5-35.7 % digital DNA-DNA hybridization values with the three type strains of Tepidibacter species. Cells of strain SWIR-1T were Gram-stain-positive, motile, short straight rods. Endospores were observed in stationary-phase cells when grown on Thermococcales rich medium. Strain SWIR-1T grew at 15-45 °C (optimum, 30°C), at pH 5.5-8.0 (optimum, pH 7.0) and with 1.0-6.0 % (w/v) NaCl (optimum, 2.0 %). Substrates utilized by strain SWIR-1T included complex proteinaceous, chitin, starch, lactose, maltose, fructose, galactose, glucose, rhamnose, arabinose, ribose, alanine, glycine and glycerol. The major fermentation products from glucose were acetate, lactate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and FeCl3 are not used as terminal electron acceptors. The main cellular fatty acids consisted of iso-C15 : 0 (28.4 %), C15 : 1 iso F (15.4 %) and C16 : 0 (9.8 %). The major polar lipids were phospholipids and glycolipids. No respiratory quinones were detected. Genomic comparison revealed a distinctive blended gene cluster comprising hyb-tat-hyp genes, which play a crucial role in the synthesis, maturation, activation and export of NiFe-hydrogenase. Based on the phylogenetic analysis, genomic, physiologic and chemotaxonomic characteristics, strain SWIR-1T is considered to represent a novel species within the genus Tepidibacter, for which the name Tepidibacter hydrothermalis sp. nov. is proposed. The type strain is strain SWIR-1T (=DSM 113848T=MCCC 1K07078T).
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Affiliation(s)
- Jie Dai
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
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Fernández Vecilla D, Roche Matheus MP, Calvo Muro FE, Iglesias Hidalgo G, Díaz de Tuesta Del Arco JL. Identification of curved Gram-negative rods by MALDI-TOF mass spectrometer in a patient with Fournier ́s gangrene. A bacteremia caused by Desulfovibrio desulfuricans and Escherichia coli. Rev Esp Quimioter 2023:fernandez28sep2023. [PMID: 37767548 DOI: 10.37201/req/026.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Clinical Microbiology and Parasitology. Hospital Universitario de Basurto. Avenida Montevideo nº18, Gurtubay pavilion, 3rd floor. Postal code: 48013, Bilbao (Basque country). Spain.
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Kajihara T, Yahara K, Kitamura N, Hirabayashi A, Hosaka Y, Sugai M. Distribution, Trends, and Antimicrobial Susceptibility of Bacteroides, Clostridium, Fusobacterium, and Prevotella Species Causing Bacteremia in Japan During 2011-2020: A Retrospective Observational Study Based on National Surveillance Data. Open Forum Infect Dis 2023; 10:ofad334. [PMID: 37469615 PMCID: PMC10352651 DOI: 10.1093/ofid/ofad334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Background The increasing prevalence of anaerobic bacteremia is a major concern worldwide and requires longitudinal monitoring. Methods We present one of the largest and longest longitudinal studies on the prevalence and antimicrobial resistance of Bacteroides, Clostridium, Fusobacterium, and Prevotella spp. isolated from blood culture samples using national comprehensive surveillance data in Japan during 2011-2020 as part of the Japan Nosocomial Infections Surveillance. Results Data for 41 949 Bacteroides spp., 40 603 Clostridium spp., 7013 Fusobacterium spp., and 5428 Prevotella spp. isolates were obtained. The incidences of bacteremia caused by Bacteroides fragilis, Clostridium perfringens, and Fusobacterium nucleatum significantly increased during the period (P < .0001). Among the 20 species analyzed, 18 showed no significant changes in susceptibility over time, including B. fragilis, C perfringens, and F. nucleatum. However, resistance to clindamycin increased in B. thetaiotaomicron (P = .0312), and resistance to ampicillin increased in B. ovatus (P = .0008). Conclusions Our comprehensive national surveillance data analysis demonstrated a continuous increase in the incidence of anaerobic bacteremia, particularly in B. fragilis, C. perfringens, and F. nucleatum. This may be linked to the increasing number of colorectal cancer cases or advancing methods for species identification and susceptibility testing, requiring cautious interpretation. The discovery of an upsurge in anaerobic bacteremia and potential alterations in susceptibility highlights the necessity for more extensive studies in this field.
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Affiliation(s)
- Toshiki Kajihara
- Correspondence: Toshiki Kajihara, MD, Phd, Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho Higashimurayama, Tokyo 189-0002, Japan ()
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Norikazu Kitamura
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yumiko Hosaka
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Kozak M, Kozak M. Commensal Streptococcal Infective Endocarditis of the Native Mitral Valve in a Transcatheter Aortic Valve Replacement (TAVR) Patient: A Heartful, a Handful, and a Mouthful. Cureus 2023; 15:e42565. [PMID: 37637617 PMCID: PMC10460250 DOI: 10.7759/cureus.42565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
An 88-year-old woman with an extensive medical history presented to the hospital with altered mental status, vague abdominal pain, and dysuria. A previous transcatheter aortic valve replacement (TAVR) prosthesis was known to be failing and was suspected to have acquired a vegetation. No other infective endocarditis (IE) stigmata were present. Fortunately, the work-up for replacement was allowed to proceed with a broader cardiac examination from which a mitral vegetation was identified and IE then treated.
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Affiliation(s)
- Michael Kozak
- Internal Medicine, Penn State College of Medicine, Hershey, USA
| | - Mark Kozak
- Cardiovascular Medicine, Penn State College of Medicine, Hershey, USA
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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. bioRxiv 2023:2023.06.26.546640. [PMID: 37425791 PMCID: PMC10327067 DOI: 10.1101/2023.06.26.546640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogen Clostridioides difficile outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
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Poothong S, Tanasupawat S, Chanpongsang S, Phongsopitanun W, Nuengjamnong C. Selenomonas caprae sp. nov., an obligately anaerobic and volatile fatty acid producing bacterium from ruminal fluid of domestic goat ( Capra hircus L.). Int J Syst Evol Microbiol 2023; 73. [PMID: 37339073 DOI: 10.1099/ijsem.0.005936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
A novel Gram-stain-negative, motile, obligately anaerobic bacterium strain mPRGC8T was isolated from the ruminal fluid of a domestic goat (Capra hircus L.) in Nakhon Pathom province, Thailand. The strain grew at 20-45 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.5) and 3 % (w/v) NaCl. It produced acetate, propionate, valerate, caproate and heptanoate from glucose. The 16S rRNA gene sequence analysis indicated that strain mPRGC8T belonged to the genus Selenomonas and was closely related to Selenomonas ruminantium subsp. ruminantium DSM 2150T (98.0 %) and Selenomonas ruminantium subsp. lactilytica JCM 6582T (97.9 %). The in silico DNA G+C content was 53.0 mol %. Strain mPRGC8T showed average nucleotide identity, digital DNA-DNA hybridization and average animo acid identity values with Selenomonas montiformis JCM 34373T, S. ruminantium subsp. lactilytica JCM 6582T and S. ruminantium subsp. ruminantium DSM 2150T ranging from 84.9 to 86.0 %, 21.3 to 21.8 % and 73.8 to 76.1 %, respectively. The predominant cellular fatty acids were C16 : 1 ω9c and C18 : 1 ω9c. Phosphatidylethanolamine, three unidentified aminophospholipids, two unidentified ninhydrin positive glycolipids, an unidentified phospholipid and an unidentified lipid were detected as polar lipids. The genomic and phenotypic characteristics of strain mPRGC8T strongly support its classification as representative of new species of the genus Selenomonas for which the name Selenomonas caprae sp. nov. is proposed. The type strain is mPRGC8T (=JCM 33725T=KCTC 25178T).
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Affiliation(s)
- Saranporn Poothong
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somchai Chanpongsang
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chackrit Nuengjamnong
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Food and Water Risk Analysis (FAWRA), Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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Grenda T, Jarosz A, Sapała M, Grenda A, Patyra E, Kwiatek K. Clostridium perfringens-Opportunistic Foodborne Pathogen, Its Diversity and Epidemiological Significance. Pathogens 2023; 12:768. [PMID: 37375458 DOI: 10.3390/pathogens12060768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The C. perfringens species is associated with various environments, such as soils, sewage, and food. However, it is also a component of the gastrointestinal (GI) microflora (i.e., microbiota) of sick and healthy humans and animals. C. perfringens is linked with different systemic and enteric diseases in livestock and humans, such as gas gangrene, food poisoning, non-foodborne diarrhoea, and enterocolitis. The strains of this opportunistic pathogen are known to secrete over 20 identified toxins that are considered its principal virulence factors. C. perfringens belongs to the anaerobic bacteria community but can also survive in the presence of oxygen. The short time between generations, the multi-production capability of toxins and heat-resistant spores, the location of many virulence genes on mobile genetic elements, and the inhabitance of this opportunistic pathogen in different ecological niches make C. perfringens a very important microorganism for public health protection. The epidemiological evidence for the association of these strains with C. perfringens-meditated food poisoning and some cases of non-foodborne diseases is very clear and well-documented. However, the genetic diversity and physiology of C. perfringens should still be studied in order to confirm the importance of suspected novel virulence traits. A very significant problem is the growing antibiotic resistance of C. perfringens strains. The aim of this review is to show the current basic information about the toxins, epidemiology, and genetic and molecular diversity of this opportunistic pathogen.
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Affiliation(s)
- Tomasz Grenda
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Aleksandra Jarosz
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Magdalena Sapała
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Anna Grenda
- Department of Pneumonology, Oncology and Allergology, Medical University in Lublin, Jaczewskiego 8, 20-950 Lublin, Poland
| | - Ewelina Patyra
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
| | - Krzysztof Kwiatek
- Department of Hygiene of Animal Feeding Stuffs, National Veterinary Research Institute in Pulawy, Partyzantow 57, 24-100 Pulawy, Poland
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Morton AB, Boyle E, Pettengill MA, Gancher E. The Brief Case: Strictly Anaerobic and Staining Acid Fast. J Clin Microbiol 2023; 61:e0015022. [PMID: 37219093 PMCID: PMC10204630 DOI: 10.1128/jcm.00150-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Arianna B. Morton
- Thomas Jefferson University Hospital, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania, USA
| | - Evan Boyle
- Thomas Jefferson University Hospital, Division of Infectious Diseases, Philadelphia, Pennsylvania, USA
| | - Matthew A. Pettengill
- Thomas Jefferson University Hospital, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania, USA
| | - Elizabeth Gancher
- Thomas Jefferson University Hospital, Division of Infectious Diseases, Philadelphia, Pennsylvania, USA
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16
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Maki JJ, Howard M, Connelly S, Pettengill MA, Hardy DJ, Cameron A. Species Delineation and Comparative Genomics within the Campylobacter ureolyticus Complex. J Clin Microbiol 2023; 61:e0004623. [PMID: 37129508 DOI: 10.1128/jcm.00046-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Campylobacter ureolyticus is an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates. We reviewed the epidemiology of clinical C. ureolyticus cultured by our institution over the past 10 years. Fifty-one unique C. ureolyticus isolates were identified between January 2010 and August 2022, mostly originating from abscesses and blood cultures. To clarify the taxonomic relationships between isolates and to attribute specific genes with different clinical manifestations, we sequenced 19 available isolates from a variety of clinical specimen types and conducted a pangenomic analysis with publicly available C. ureolyticus genomes. Digital DNA:DNA hybridization suggested that these C. ureolyticus comprised a species complex of 10 species clusters (SCs) and several subspecies clusters. Although some orthologous genes or gene functions were enriched in isolates found in different SCs and clinical specimens, no association was significant. Nearly a third of the isolates possessed antimicrobial resistance genes, including the ermA resistance gene, potentially conferring resistance to macrolides, the treatment of choice for severe human campylobacteriosis. This work effectively doubles the number of publicly available C. ureolyticus genomes, provides further clarification of taxonomic relationships within this bacterial complex, and identifies target SCs for future analysis.
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Affiliation(s)
- Joel J Maki
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Mondraya Howard
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Sara Connelly
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Matthew A Pettengill
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Dwight J Hardy
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
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Zhang SM, Huang SL. The Commensal Anaerobe Veillonella dispar Reprograms Its Lactate Metabolism and Short-Chain Fatty Acid Production during the Stationary Phase. Microbiol Spectr 2023; 11:e0355822. [PMID: 36975840 PMCID: PMC10100942 DOI: 10.1128/spectrum.03558-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 02/20/2023] [Indexed: 03/29/2023] Open
Abstract
Veillonella spp. are obligate, anaerobic, Gram-negative bacteria found in the human oral cavity and gut. Recent studies have indicated that gut Veillonella promote human homeostasis by producing beneficial metabolites, specifically short-chain fatty acids (SCFAs), by lactate fermentation. The gut lumen is a dynamic environment with fluctuating nutrient levels, so the microbes present shifting growth rates and significant variations of gene expression. The current knowledge of lactate metabolism by Veillonella has focused on log phase growth. However, the gut microbes are mainly in the stationary phase. In this study, we investigated the transcriptomes and major metabolites of Veillonella dispar ATCC 17748T during growth from log to stationary phases with lactate as the main carbon source. Our results revealed that V. dispar reprogrammed its lactate metabolism during the stationary phase. Lactate catabolic activity and propionate production were significantly decreased during the early stationary phase but were partially restored during the stationary phase. The propionate/acetate production ratio was lowered from 1.5 during the log phase to 0.9 during the stationary phase. Pyruvate secretion was also greatly decreased during the stationary phase. Furthermore, we have demonstrated that the gene expression of V. dispar is reprogrammed during growth, as evidenced by the distinct transcriptomes present during the log, early stationary, and stationary phases. In particular, propionate metabolism (the propanediol pathway) was downregulated during the early stationary phase, which explains the decrease in propionate production during the stationary phase. The fluctuations in lactate fermentation during the stationary phase and the associated gene regulation expand our understanding of the metabolism of commensal anaerobes in changing environments. IMPORTANCE Short-chain fatty acids produced by gut commensal bacteria play an important role in human physiology. Gut Veillonella and the metabolites acetate and propionate, produced by lactate fermentation, are associated with human health. Most gut bacteria in humans are in the stationary phase. Lactate metabolism by Veillonella spp. during the stationary phase is poorly understood and was therefore the focus of the study. To this end, we used a commensal anaerobic bacterium and explored its short-chain fatty acid production and gene regulation in order to provide a better understanding of lactate metabolism dynamics during nutrient limitation.
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Affiliation(s)
- Shi-Min Zhang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Yangming Campus, Taipei, Taiwan
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Yangming Campus, Taipei, Taiwan
| | - Shir-Ly Huang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Yangming Campus, Taipei, Taiwan
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Meslé MM, Gray CR, Dlakić M, DuBois JL. Bacteroides thetaiotaomicron, a Model Gastrointestinal Tract Species, Prefers Heme as an Iron Source, Yields Protoporphyrin IX as a Product, and Acts as a Heme Reservoir. Microbiol Spectr 2023; 11:e0481522. [PMID: 36862015 PMCID: PMC10100974 DOI: 10.1128/spectrum.04815-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
Members of the phylum Bacteroidetes are abundant in healthy gastrointestinal (GI) tract flora. Bacteroides thetaiotaomicron is a commensal heme auxotroph and representative of this group. Bacteroidetes are sensitive to host dietary iron restriction but proliferate in heme-rich environments that are also associated with colon cancer. We hypothesized that B. thetaiotaomicron may act as a host reservoir for iron and/or heme. In this study, we defined growth-promoting quantities of iron for B. thetaiotaomicron. B. thetaiotaomicron preferentially consumed and hyperaccumulated iron in the form of heme when presented both heme and nonheme iron sources in excess of its growth needs, leading to an estimated 3.6 to 8.4 mg iron in a model GI tract microbiome consisting solely of B. thetaiotaomicron. Protoporphyrin IX was identified as an organic coproduct of heme metabolism, consistent with anaerobic removal of iron from the heme leaving the intact tetrapyrrole as the observed product. Notably, no predicted or discernible pathway for protoporphyrin IX generation exists in B. thetaiotaomicron. Heme metabolism in congeners of B. thetaiotaomicron has previously been associated with the 6-gene hmu operon, based on genetic studies. A bioinformatics survey demonstrated that the intact operon is widespread in but confined to members of the Bacteroidetes phylum and ubiquitous in healthy human GI tract flora. Anaerobic heme metabolism by commensal Bacteroidetes via hmu is likely a major contributor to human host metabolism of the heme from dietary red meat and a driver for the selective growth of these species in the GI tract consortium. IMPORTANCE Research on bacterial iron metabolism has historically focused on the host-pathogen relationship, where the host suppresses pathogen growth by cutting off access to iron. Less is known about how host iron is shared with bacterial species that live commensally in the anaerobic human GI tract, typified by members of phylum Bacteroidetes. While many facultative pathogens avidly produce and consume heme iron, most GI tract anaerobes are heme auxotrophs whose metabolic preferences we aimed to describe. Understanding iron metabolism by model microbiome species like Bacteroides thetaiotaomicron is essential for modeling the ecology of the GI tract, which serves the long-term biomedical goals of manipulating the microbiome to facilitate host metabolism of iron and remediate dysbiosis and associated pathologies (e.g., inflammation and cancer).
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Affiliation(s)
- Margaux M. Meslé
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Chase R. Gray
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Mensur Dlakić
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Yoshimatsu Y, Aga M, Komiya K, Haranaga S, Numata Y, Miki M, Higa F, Senda K, Teramoto S. The Clinical Significance of Anaerobic Coverage in the Antibiotic Treatment of Aspiration Pneumonia: A Systematic Review and Meta-Analysis. J Clin Med 2023; 12. [PMID: 36902779 DOI: 10.3390/jcm12051992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
INTRODUCTION Aspiration pneumonia is increasingly recognised as a common condition. While antibiotics covering anaerobes are thought to be necessary based on old studies reporting anaerobes as causative organisms, recent studies suggest that it may not necessarily benefit prognosis, or even be harmful. Clinical practice should be based on current data reflecting the shift in causative bacteria. The aim of this review was to investigate whether anaerobic coverage is recommended in the treatment of aspiration pneumonia. METHODS A systematic review and meta-analysis of studies comparing antibiotics with and without anaerobic coverage in the treatment of aspiration pneumonia was performed. The main outcome studied was mortality. Additional outcomes were resolution of pneumonia, development of resistant bacteria, length of stay, recurrence, and adverse effects. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines were followed. RESULTS From an initial 2523 publications, one randomised control trial and two observational studies were selected. The studies did not show a clear benefit of anaerobic coverage. Upon meta-analysis, there was no benefit of anaerobic coverage in improving mortality (Odds ratio 1.23, 95% CI 0.67-2.25). Studies reporting resolution of pneumonia, length of hospital stay, recurrence of pneumonia, and adverse effects showed no benefit of anaerobic coverage. The development of resistant bacteria was not discussed in these studies. CONCLUSION In the current review, there are insufficient data to assess the necessity of anaerobic coverage in the antibiotic treatment of aspiration pneumonia. Further studies are needed to determine which cases require anaerobic coverage, if any.
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Jiao ZX, Li XG, Zhang HH, Xu J, Bai SJ, Dai J, Lin J, Zhang WJ, Qi XQ, Wu LF. Crassaminicella indica sp. nov., a novel thermophilic anaerobic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2023; 73. [PMID: 36951905 DOI: 10.1099/ijsem.0.005725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
A novel moderately thermophilic heterotrophic bacterium, designated strain 143-21T, was isolated from a deep-sea hydrothermal chimney sample collected from the Central Indian Ridge at a depth of 2 440 m. Phylogenetic analysis indicated that strain 143-21T belongs to the genus Crassaminicella. It was most closely related to Crassaminicella thermophila SY095T (96.79 % 16S rRNA gene sequence similarity) and Crassaminicella profunda Ra1766HT (96.52 %). Genomic analysis showed that strain 143-21T shares 79.79-84.45 % average nucleotide identity and 23.50-29.20 % digital DNA-DNA hybridization with the species of the genus Crassaminicella, respectively. Cells were rod-shaped, non-motile, Gram-positive-staining. Terminal endospores were observed in stationary-phase cells when strain 143-21T was grown on Thermococcales rich medium. Strain 143-21T was able to grow at 30-60 °C (optimum, 50 °C), pH 6.5-8.5 (optimum, pH 7.0) and in 1.0-7.0 % NaCl (w/v; optimum 2.0 %, w/v). Strain 143-21T utilized fructose, glucose, maltose, mannose, ribose, N-acetyl-d-(+)-glucosamine and casamino acids, as well as amino acids including glutamate, lysine, histidine and cysteine. The main fermentation products from glucose were acetate (2.07 mM), H2 and CO2. It did not reduce elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe (III). The predominant cellular fatty acids were C14 : 0 (48.8 %), C16 : 0 (12.9 %), and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 10.2 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, as well as two unidentified phospholipids and four unidentified aminolipids. No respiratory quinones were detected. Based on its phylogenetic analysis and physiological characteristics, strain 143-21T is considered to represent a novel species of the genus Crassaminicella, for which the name Crassaminicella indica sp. nov. is proposed. The type strain is strain 143-21T (=DSM 114408T= MCCC 1K06400T).
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Affiliation(s)
- Ze-Xi Jiao
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, Marseille-Beijing-Qingdao-Sanya, Qingdao
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Institution of Deep-sea Life Sciences, Sanya, Hainan, PR China
| | - Huan-Huan Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Shi-Jie Bai
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- Laboratory of Marine Viruses and Molecular Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Jie Dai
- CNRS, LCB, IMM, IM2B, Aix Marseille Univ, Marseille, France
| | - Jin Lin
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, Marseille-Beijing-Qingdao-Sanya, Qingdao
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Institution of Deep-sea Life Sciences, Sanya, Hainan, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, Marseille-Beijing-Qingdao-Sanya, Qingdao
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, Marseille-Beijing-Qingdao-Sanya, Qingdao
- CNRS, LCB, IMM, IM2B, Aix Marseille Univ, Marseille, France
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Lawson PA, Saavedra Perez L, Sankaranarayanan K. Reclassification of Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia as Thomasclavelia cocleata gen. nov., comb. nov., Thomasclavelia ramosa comb. nov., gen. nov., Thomasclavelia spiroformis comb. nov. and Thomasclavelia saccharogumia comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748617 DOI: 10.1099/ijsem.0.005694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genus Clostridium is phenotypically and genotypically diverse, with many species phylogenetically located outside Clostridium sensu stricto. One such group consists of the species Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia (formally clostridial rRNA cluster XVIII) [1]. Sequencing of the 16S rRNA and, more recently, the results of genomic analyses have demonstrated that these species represent a coherent cluster separated from other closely related genera located in the family Coprobacillaceae within the order Erysipelotrichales [2]. In addition to phenotypic, phylogenetic and genomic comparisons, chemotaxonomic features were consistent between all four species, the predominant fatty acids were C16 : 0 and C18 : 1ω9c, while glucose and ribose were the whole cell sugars present in the cell walls. Furthermore, he results of peptidoglycan analysis indicated that meso-2,6-diaminopimelic acid was present as the diagnostic diamino acid in all four species. Biochemical profiles were also concordant with them being closely related species. Therefore, on the basis of phylogenetic, genomic, phenotypic and chemotaxonomic information, a novel genus, Thomasclavelia gen. nov., is proposed. It is suggested that Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia be transferred to this genus as Thomasclavelia cocleata comb. nov., Thomasclavelia ramosa comb. nov., Thomasclavelia saccharogumia comb. nov. and Thomasclavelia spiroformis comb. nov. The type species of the genus is Thomasclavelia ramosa CCUG 24038T (=ATCC 25582T=DSM 1402T).
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Affiliation(s)
- Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Liz Saavedra Perez
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,Present address: Molecular & Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine 04469-5735, USA
| | - Krithivasan Sankaranarayanan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
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Popoff MR, Legout S. Anaerobes and Toxins, a Tradition of the Institut Pasteur. Toxins (Basel) 2023; 15:43. [PMID: 36668863 PMCID: PMC9861305 DOI: 10.3390/toxins15010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Louis Pasteur, one of the eminent pioneers of microbiology, discovered life without oxygen and identified the first anaerobic pathogenic bacterium. Certain bacteria were found to be responsible for specific diseases. Pasteur was mainly interested in the prevention and treatment of infectious diseases with attenuated pathogens. The collaborators of Pasteur investigated the mechanisms of pathogenicity and showed that some bacterial soluble substances, called toxins, induce symptoms and lesions in experimental animals. Anaerobic bacteriology, which requires specific equipment, has emerged as a distinct part of microbiology. The first objectives were the identification and taxonomy of anaerobes. Several anaerobes producing potent toxins were associated with severe diseases. The investigation of toxins including sequencing, mode of action, and enzymatic activity led to a better understanding of toxin-mediated pathogenicity and allowed the development of safe and efficient prevention and treatment (vaccination with anatoxins, specific neutralizing antisera). Moreover, toxins turned out to be powerful tools in exploring cellular mechanisms supporting the concept of cellular microbiology. Pasteurians have made a wide contribution to anaerobic bacteriology and toxinology. The historical steps are summarized in this review.
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Affiliation(s)
| | - Sandra Legout
- Centre de Ressources en Information Scientifique, Institut Pasteur, 75015 Paris, France
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Hosin N, Abu-Ali BM, Al Rashed AS, Al-Warthan SM, Diab AE. Clostridium paraputrificum Bacteremia in a Patient with Human Immunodeficiency Virus Infection: A Case Report and Literature Review. Infect Drug Resist 2023; 16:1449-1454. [PMID: 36942023 PMCID: PMC10024499 DOI: 10.2147/idr.s400490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/15/2023] Open
Abstract
Clostridium paraputrificum (C. paraputrificum) is clinically important due to its association with underlying medical conditions. Infection with C. paraputrificum may worsen HIV prognosis, leading to acquired immunodeficiency syndrome. However, it is not frequently isolated and its susceptibility to antibiotics has not been well studied. Our report examines the case of a patient with human immunodeficiency virus (HIV) infection, who was diagnosed with Clostridium paraputrificum bacteremia. A 59-year-old male was admitted to hospital with a medical history of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and neck pain. Following episodes of high fever, the patient received a full work up to test for sepsis. Blood culture revealed bacterial growth, and MALDI-TOF mass spectrometry confirmed the diagnosis of Clostridium paraputrificum bacteremia. The patient received treatment with meropenem and vancomycin antibiotics, which cleared the infection after 48 hours; however, inflammatory markers remained high. To date, a limited number of reported cases of C. paraputrificum exist; thus, this case report contributes valuable information to the literature to improve our understanding of its action and resistance profiles and aid future bacteremia management.
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Affiliation(s)
- Nehal Hosin
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Batool M Abu-Ali
- Department of Internal Medicine, Infectious Diseases Division, King Fahad Hospital, Hofuf, Saudi Arabia
| | - Abdullatif S Al Rashed
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Correspondence: Abdullatif S Al Rashed, Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia, Tel +966555969048, Email
| | - Sara M Al-Warthan
- Department of Internal Medicine, King Fahd Hospital of the University (Imam Abdulrahman Bin Faisal University), Al Khobar, Saudi Arabia
| | - Asim E Diab
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Vecilla DF, López IA, Yanes MLG, Toboso MCN, del Arco JLDDT. Is Propionimicrobium lymphophilum a new urinary tract infection cause? Rev Esp Quimioter 2023; 36:107-109. [PMID: 36458724 PMCID: PMC9910668 DOI: 10.37201/req/086.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Domingo Fernández Vecilla
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Correspondence: Domingo Fernández Vecilla, Clinical Microbiology and Parasitology. Hospital Universitario de Basurto. Avenida Montevideo nº18, Gurtubay pavilion, 3rd floor. Postal code: 48013, Bilbao (Basque country). Spain. E-mail:
| | - Itziar Angulo López
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - María Luisa Gurruchaga Yanes
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - María Carmen Nieto Toboso
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - José Luis Díaz de Tuesta del Arco
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
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25
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Javier-Lopez R, Mandolini E, Dzhuraeva M, Bobodzhanova K, Birkeland NK. Fervidobacterium pennivorans subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile. Microorganisms 2022; 11. [PMID: 36677314 DOI: 10.3390/microorganisms11010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Fervidobacterium pennivorans subsp. keratinolyticus subsp. nov. strain T was isolated from a terrestrial, high-altitude hot spring in Tajikistan. This strain is an obligate anaerobic rod and their cells occur singly, in pairs, or as short chains under the optimal growth conditions of a temperature of 65 °C and pH 6.5, with peptone, glucose, and galactose as the preferred substrates. The minimum generation time of this strain is 150 min. Strain T can efficiently degrade feather keratin at 65-75 °C; this unusual feature is also exhibited by a few other members of the Fervidobacterium genus. The total genome size of this bacterial strain is 2,002,515 base pairs, with a C + G content of 39.0%. The maximum digital DNA-DNA hybridization (dDDH) value of 76.9% was observed on comparing the genome of this strain with that of Fervidobacterium pennivorans type strain DSM9078. This study describes the physiological and genomic properties of strain T, with an emphasis on its keratinolytic power and differences from other members of the genus Fervidobacterium.
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26
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Abstract
Pott's puffy tumor, a rare condition, is an osteomyelitis involving the frontal bone with accompanying subperiosteal abscess. Patients typically present with swelling of the scalp and forehead, headache, fever, tenderness of the frontal sinus, and nasal discharge. MRI is the modality of choice for diagnosis and assessment. The standard of care is incision and drainage with long-course antibiotics. The prognosis is excellent; however, complications from a hematogenous spread can lead to meningitis or epidural spaces if not treated properly.
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27
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Palabikyan H, Ruddyard A, Pomper L, Novak D, Reischl B, Rittmann SKMR. Scale-up of biomass production by Methanococcus maripaludis. Front Microbiol 2022; 13:1031131. [PMID: 36504798 PMCID: PMC9727139 DOI: 10.3389/fmicb.2022.1031131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD578) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h-1 and the highest recorded OD578 of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.
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Affiliation(s)
- Hayk Palabikyan
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - Aquilla Ruddyard
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Lara Pomper
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Barbara Reischl
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,*Correspondence: Simon K.-M. R. Rittmann,
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28
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Wang Y, Liu Z, Chen Q, Yi L, Xu Z, Cai M, Qin J, Zhang Y, Du G, Hong J, Guo X, Liu C. Isolation and characterization of novel Fusobacterium nucleatum bacteriophages. Front Microbiol 2022; 13:945315. [PMID: 36406437 PMCID: PMC9670143 DOI: 10.3389/fmicb.2022.945315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/06/2022] [Indexed: 10/03/2023] Open
Abstract
Fusobacterium nucleatum is a strictly anaerobic, Gram-negative bacterial species that is a member of the commensal flora in the oral cavity and gut. Recent studies suggested that the increase of abundance is associated with the development of various diseases, among which colorectal cancer is of the biggest concerns. Phage therapy is regarded as a potential approach to control the number of F. nucleatum, which may contribute to the prevention and treatment of related diseases. In this study, we isolated five isolates of bacteriophage targeting F. nucleatum. The morphological, biological, genomic and functional characteristics of five bacteriophages were investigated. Transmission electron microscopy revealed that JD-Fnp1 ~ JD-Fnp5 are all myoviruses. The size of the JD-Fnp1 ~ JD-Fnp5 genomes was 180,066 bp (JD-Fnp1), 41,329 bp (JD-Fnp2), 38,962 bp (JD-Fnp3), 180,231 bp (JD-Fnp4), and 41,353 bp (JD-Fnp5) respectively. The biological features including pH and heat stability, host range, growth characteristics of JD-Fnp1 ~ JD-Fnp5 displayed different patterns. Among them, JD-Fnp4 is considered to have the greatest clinical application value. The identification and characterization of JD-Fnp1 ~ JD-Fnp5 provides a basis for subsequent therapeutic strategy exploration of F. nucleatum-related diseases.
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Affiliation(s)
- Yue Wang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhitong Liu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Chen
- Research Institute of Intestinal Diseases, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liqi Yi
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zihao Xu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mufeng Cai
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinhong Qin
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guanhuan Du
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
| | - Chang Liu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Slobodkina G, Ratnikova N, Merkel A, Kevbrin V, Kuchierskaya A, Slobodkin A. Lithoautotrophic lifestyle of the widespread genus Roseovarius revealed by physiological and genomic characterization of Roseovarius autotrophicus sp. nov. FEMS Microbiol Ecol 2022; 98:6724241. [PMID: 36166357 DOI: 10.1093/femsec/fiac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/13/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
The genus Roseovarius, a member of the ecologically important Roseobacter-clade, is widespread throughout the world. A facultatively anaerobic lithoautotrophic bacterium (strain SHN287T), belonging to the genus Roseovarius, was isolated with molecular hydrogen as an electron donor and nitrate as an electron acceptor from a terrestrial mud volcano. Strain SHN287T possessed metabolic features not reported for Roseovarius such as chemolithoautotrophic growth with oxidation of molecular hydrogen or sulfur compounds, anaerobic growth and denitrification. Based on the phenotypic and phylogenetic characteristics, the new isolate is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius autotrophicus sp. nov. is proposed. The type strain is SHN287T (= KCTC 15916T = VKM B-3404T). An amended description of the genus Roseovarius is provided. Comparison of 46 Roseovarius genomes revealed that (i) a full set of genes for the Calvin-Benson cycle is present only in two strains: SHN287T and Roseovarius salinarum; (ii) respiratory H2-uptake [NiFe] hydrogenases are specific for a phylogenetically distinct group, including SHN287T-related strains; (iii) the Sox enzymatic complex is encoded in most of the studied genomes; and (iv) denitrification genes are widespread and randomly distributed among the genus. The metabolic characteristics found in R. autotrophicus sp. nov. expand the ecological role of the genus Roseovarius.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Nataliya Ratnikova
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - Vadim Kevbrin
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | | | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, FRC Biotechnology Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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30
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Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, Franz CMAP. Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5. Viruses 2022; 14:v14081598. [PMID: 35893664 PMCID: PMC9394477 DOI: 10.3390/v14081598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
- Correspondence:
| | - Torben S. Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Finn K. Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Dennis S. Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
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31
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Abstract
The ability of the anaerobic gastrointestinal pathogen Clostridioides difficile to survive outside the host relies on the formation of dormant endospores. Spore formation is contingent on the activation of a conserved transcription factor, Spo0A, by phosphorylation. Multiple kinases and phosphatases regulate Spo0A activity in other spore-forming organisms; however, these factors are not well conserved in C. difficile. Previously, we discovered that deletion of a predicted histidine kinase, CD1492, increases sporulation, indicating that CD1492 inhibits C. difficile spore formation. In this study, we investigate the functions of additional predicted orphan histidine kinases CD2492, CD1579, and CD1949, which are hypothesized to regulate Spo0A phosphorylation. Disruption of CD2492 also increased sporulation frequency, similarly to the CD1492 mutant and in contrast to a previous study. A CD1492 CD2492 mutant phenocopied the sporulation and gene expression patterns of the single mutants, suggesting that these proteins function in the same genetic pathway to repress sporulation. Deletion of CD1579 variably increased sporulation frequency; however, knockdown of CD1949 expression did not influence sporulation. We provide evidence that CD1492, CD2492, and CD1579 function as phosphatases, as mutation of the conserved histidine residue for phosphate transfer abolished CD2492 function, and expression of the CD1492 or CD2492 histidine site-directed mutants or the wild-type CD1579 allele in a parent strain resulted in a dominant-negative hypersporulation phenotype. Altogether, at least three predicted histidine kinases, CD1492, CD2492, and CD1579 (herein, PtpA, PtpB and PtpC), repress C. difficile sporulation initiation by regulating activity of Spo0A. IMPORTANCE The formation of inactive spores is critical for the long-term survival of the gastrointestinal pathogen Clostridioides difficile. The onset of sporulation is controlled by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple kinases and phosphatases control Spo0A phosphorylation; however, this regulatory pathway is not defined in C. difficile. We show that two predicted histidine kinase proteins, CD1492 (PtpA) and CD2492 (PtpB), function in the same regulatory pathway to repress sporulation by preventing Spo0A phosphorylation. We show that another predicted histidine kinase protein, CD1579 (PtpC), also represses sporulation and present evidence that a fourth predicted histidine kinase protein, CD1949, does not impact sporulation. These results support the idea that C. difficile inhibits sporulation initiation through multiple phosphatases.
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32
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Baumann LMF, Taubner RS, Oláh K, Rohrweber AC, Schuster B, Birgel D, Rittmann SKMR. Quantitative Analysis of Core Lipid Production in Methanothermobacter marburgensis at Different Scales. Bioengineering (Basel) 2022; 9:169. [PMID: 35447729 PMCID: PMC9027985 DOI: 10.3390/bioengineering9040169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeal lipids have a high biotechnological potential, caused by their high resistance to oxidative stress, extreme pH values and temperatures, as well as their ability to withstand phospholipases. Further, methanogens, a specific group of archaea, are already well-established in the field of biotechnology because of their ability to use carbon dioxide and molecular hydrogen or organic substrates. In this study, we show the potential of the model organism Methanothermobacter marburgensis to act both as a carbon dioxide based biological methane producer and as a potential supplier of archaeal lipids. Different cultivation settings were tested to gain an insight into the optimal conditions to produce specific core lipids. The study shows that up-scaling at a constant particle number (n/n = const.) seems to be a promising approach. Further optimizations regarding the length and number of the incubation periods and the ratio of the interaction area to the total liquid volume are necessary for scaling these settings for industrial purposes.
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Affiliation(s)
- Lydia M. F. Baumann
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Ruth-Sophie Taubner
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
- Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, Altenbergerstraße 69, 4040 Linz, Austria
| | - Kinga Oláh
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Ann-Cathrin Rohrweber
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; (K.O.); (B.S.)
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, Bundesstraße 55, 20146 Hamburg, Germany; (L.M.F.B.); (A.-C.R.); (D.B.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria;
- Arkeon GmbH, Technopark 1, 3430 Tulln an der Donau, Austria
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33
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Abstract
Three novel, anaerobic, Gram-positive bacteria were isolated from the eggshell of two separate white leghorn chicken flocks and the ileum of a healthy pig, and designated MMM721T, ISU324 and PIG517 respectively. Cells were pleomorphic and capable of forming long chains of rods or coccoid clusters. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains to be within the genus Turicibacter, of which only one species, Turicibacter sanguinis, has been formally described. However, whole genome sequencing of novel isolates returned a digital DNA-DNA hybridization value of 22.5 % and average nucleotide identity (ANI) values of 76.4 % (ANIb) and 86.0 % (ANIm), indicating divergence between the type strain MMM721T and T. sanguinis, suggesting the strains represented a novel species. The major fatty acid methyl esters of strain MMM721T were C16 : 0, C18 : 1 ω7c and C18 : 0. The strains mainly produced the volatile fatty acid lactate, along with smaller amounts of acetate and butyrate. Together, these data indicate that MMM721T, along with ISU324 and PIG517, represent a novel species within the genus Turicibacter. We propose the name Turicibacter bilis sp. nov. for the species. The type strain is MMM721T (=ATCC TSD-238T=CCUG 74757T).
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Affiliation(s)
- Joel J Maki
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, Tennessee 37830, USA
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
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34
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Abstract
The formation of dormant spores is essential for the anaerobic pathogen Clostridioides difficile to survive outside the host gastrointestinal tract. The regulatory pathways and environmental signals that initiate C. difficile spore formation within the host are not well understood. One second-messenger signaling molecule, cyclic diguanylate (c-di-GMP), modulates several physiological processes important for C. difficile pathogenesis and colonization, but the impact of c-di-GMP on sporulation is unknown. In this study, we investigated the contribution of c-di-GMP to C. difficile sporulation. The overexpression of a gene encoding a diguanylate cyclase, dccA, decreased the sporulation frequency and early sporulation gene transcription in both the epidemic R20291 and historical 630Δerm strains. The expression of a dccA allele encoding a catalytically inactive DccA that is unable to synthesize c-di-GMP no longer inhibited sporulation, indicating that the accumulation of intracellular c-di-GMP reduces C. difficile sporulation. A null mutation in dccA slightly increased sporulation in R20291 and slightly decreased sporulation in 630Δerm, suggesting that DccA contributes to the intracellular pool of c-di-GMP in a strain-dependent manner. However, these data were highly variable, underscoring the complex regulation involved in modulating intracellular c-di-GMP concentrations. Finally, the overexpression of dccA in known sporulation mutants revealed that c-di-GMP is likely signaling through an unidentified regulatory pathway to control early sporulation events in C. difficile. c-di-GMP-dependent regulation of C. difficile sporulation may represent an unexplored avenue of potential environmental and intracellular signaling that contributes to the complex regulation of sporulation initiation. IMPORTANCE Many bacterial organisms utilize the small signaling molecule cyclic diguanylate (c-di-GMP) to regulate important physiological processes, including motility, toxin production, biofilm formation, and colonization. c-di-GMP inhibits motility and toxin production and promotes biofilm formation and colonization in the anaerobic, gastrointestinal pathogen Clostridioides difficile. However, the impact of c-di-GMP on C. difficile spore formation, a critical step in this pathogen's life cycle, is unknown. Here, we demonstrate that c-di-GMP negatively impacts sporulation in two clinically relevant C. difficile strains, the epidemic strain R20291 and the historical strain 630Δerm. The pathway through which c-di-GMP controls sporulation was investigated, and our results suggest that c-di-GMP is likely signaling through an unidentified regulatory pathway to control C. difficile sporulation. This work implicates c-di-GMP metabolism as a mechanism to integrate environmental and intracellular cues through c-di-GMP levels to influence C. difficile sporulation.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Caitlin L. Willams
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nivedita Pareek
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, North Carolina, USA
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35
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Watanabe M, Kojima H, Okano K, Fukui M. Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV. Int J Syst Evol Microbiol 2021; 71. [PMID: 34874244 DOI: 10.1099/ijsem.0.005138] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600-800 nm. The temperature range for growth was 15-37 °C, with optimum growth at 30-32 °C. The pH range for growth was pH 6.2-8.9, with optimum growth at pH 7.2-7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2-3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C16:0 and anteiso-C15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae, class Mollicutes. The closest relative of strain Mahy22T with a validly published name was Acholeplasma palmae J233T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan.,Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Kunihiro Okano
- Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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36
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Abstract
Ruminococcus gnavus (R. gnavus) is a gram positive anaerobe and a member of the normal intestinal flora of humans. Here, we present a case study of bloodstream infection caused by R. gnavus in an 85 year old man. We identified R. gnavus using target DNA sequencing. The patient was treated with intravenous meropenem and ceftriaxone based on antimicrobial susceptibility tests. He recovered well and was discharged.
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Affiliation(s)
- Xin Fan
- Department of Dermatology, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Yejin Chen
- Department of Clinical Laboratory, No. 9 Hospital of Ningbo, Zhejiang, China
| | - Yanqing Liu
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Liqing Hu
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, Zhejiang, China
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37
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Li R, Zhuang W, Wang C, El-Serehy H, Al-Farraj SA, Warren A, Hu X. Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea). Int J Syst Evol Microbiol 2021; 71. [PMID: 34427553 DOI: 10.1099/ijsem.0.004936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.
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Affiliation(s)
- Ran Li
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Wenbao Zhuang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Congcong Wang
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
| | - Hamed El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Xiaozhong Hu
- College of Fisheries, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, PR China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, PR China
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38
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Swift CL, Louie KB, Bowen BP, Hooker CA, Solomon KV, Singan V, Daum C, Pennacchio CP, Barry K, Shutthanandan V, Evans JE, Grigoriev IV, Northen TR, O'Malley MA. Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship. mBio 2021; 12:e0144221. [PMID: 34399620 DOI: 10.1128/mBio.01442-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria Fibrobacter succinogenes strain UWB7 with the anaerobic gut fungi Anaeromyces robustus or Caecomyces churrovis on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription. A. robustus upregulated components of its secondary metabolism in the presence of Fibrobacter succinogenes strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both A. robustus and C. churrovis cocultures upregulated S-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present. F. succinogenes strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that A. robustus and C. churrovis produce antimicrobials when exposed to rumen bacteria and, more broadly, that anaerobic gut fungi are a source of novel antibiotics.
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Van Zuylen EM, Ferguson SA, Hughes A, Rennison D, Brimble MA, Cook GM. Disruption of Metallostasis in the Anaerobic Human Pathogen Fusobacterium nucleatum by the Zinc Ionophore PBT2. ACS Infect Dis 2021; 7:2285-2298. [PMID: 34259502 DOI: 10.1021/acsinfecdis.0c00887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Gram-negative anaerobe Fusobacterium nucleatum is an opportunistic human pathogen, most frequently associated with periodontal disease through dental biofilm formation and, increasingly, with colorectal cancer development and progression. F. nucleatum infections are routinely treated by broad-spectrum β-lactam antibiotics and metronidazole. However, these antibiotics can negatively impact the normal microflora. Therefore, the development of novel narrow-spectrum antimicrobials active against anaerobic pathogens is of great interest. Here, we examined the antimicrobial Zn ionophore PBT2, an 8-hydroxyquinoline analogue with metal chelating properties, against a single type isolate F. nucleatum ATCC 25586. PBT2-Zn was a potent inhibitor of growth and exhibited synergistic bactericidal (>3-log10 killing) activity at 5× MIC in planktonic cells, and at the MIC in biofilms grown in vitro. Physiological and transcriptional analyses uncovered a strong cellular response relating to Zn and Fe homeostasis in PBT2-Zn treated cells across subinhibitory and inhibitory concentrations. At 1× MIC, PBT2 alone induced a 3.75-fold increase in intracellular Zn, whereas PBT2-Zn challenge induced a 19-fold accumulation of intracellular Zn after 2 h. A corresponding 2.1-fold loss of Fe was observed at 1× MIC. Transcriptional analyses after subinhibitory PBT2-Zn challenge (0.125 μg/mL and 200 μM ZnSO4) revealed significant differential expression of 15 genes at 0.5 h, and 12 genes at 1 h. Upregulated genes included those with roles in Zn homeostasis (e.g., a Zn-transporting ATPase and the Zn-sensing transcriptional regulator, smtB) and hemin transport (hmuTUV) to re-establish Fe homeostasis. A concentration-dependent protective effect was observed for cells pretreated with hemin (50 μg/mL) prior to PBT2-Zn challenge. The data presented here supports our proposal that targeting the disruption of metallostasis by Zn-translocating ionophores is a strategy worth investigating further for the treatment of Gram-negative anaerobic pathogens.
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Affiliation(s)
- Essie M. Van Zuylen
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand, 9016
| | - Scott A. Ferguson
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand, 9016
| | - Alan Hughes
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand, 9016
| | - David Rennison
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand, 1010
| | - Margaret A. Brimble
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand, 1010
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand, 92019
| | - Gregory M. Cook
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand, 9016
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand, 92019
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40
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Baquer F, Ali Sawan A, Auzou M, Grillon A, Jaulhac B, Join-Lambert O, Boyer PH. Broth Microdilution and Gradient Diffusion Strips vs. Reference Agar Dilution Method: First Evaluation for Clostridiales Species Antimicrobial Susceptibility Testing. Antibiotics (Basel) 2021; 10:antibiotics10080975. [PMID: 34439025 PMCID: PMC8388896 DOI: 10.3390/antibiotics10080975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/05/2022] Open
Abstract
Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference method. In this work, we evaluated two broth microdilution kits (MICRONAUT-S Anaerobes® MIC and Sensititre Anaerobe MIC®) and one gradient diffusion strip method (Liofilchem®) for antimicrobial susceptibility testing of 47 Clostridiales isolates (Clostridium, Clostridioides and Hungatella species) using the agar dilution method as a reference. The evaluation focused on comparing six antimicrobial molecules available in both microdilution kits. Analytical performances were evaluated according to the Food and Drug Administration (FDA) recommendations. Essential agreements (EA) and categorical agreements (CA) varied greatly according to the molecule and the evaluated method. Vancomycin had values of essential and categorical agreements above 90% for the three methods. The CA fulfilled the FDA criteria for three major molecules in the treatment of Gram-positive anaerobic infections (metronidazole, piperacillin/tazobactam and vancomycin). The highest rate of error was observed for clindamycin. Multicenter studies are needed to further validate these results.
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Affiliation(s)
- Florian Baquer
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
| | - Asma Ali Sawan
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Michel Auzou
- Research Group on Microbial Adaptation GRAM 2.0, Department of Microbiology and Hygiene, Caen University Hospital of Caen, UniCaen-UniRouen, F-14033 Caen, France; (M.A.); (O.J.-L.)
| | - Antoine Grillon
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Benoît Jaulhac
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Olivier Join-Lambert
- Research Group on Microbial Adaptation GRAM 2.0, Department of Microbiology and Hygiene, Caen University Hospital of Caen, UniCaen-UniRouen, F-14033 Caen, France; (M.A.); (O.J.-L.)
| | - Pierre H. Boyer
- Laboratory of Bacteriology, Strasbourg University Hospital, F-67000 Strasbourg, France; (F.B.); (A.A.S.); (A.G.); (B.J.)
- Institute of Bacteriology, University of Strasbourg, UR7290, ITI InnoVec, Fédération de Médecine Translationnelle de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
- Correspondence:
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41
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Abstract
Mitochondrial DNA (mtDNA) is a universal hallmark of aerobic eukaryotes. That is why the recent suggestion by John et al. (2019. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci Adv. 5(4):eaav1110.) that the aerobic dinoflagellate Amoebophrya sp. strain AT5 (Syndiniales) lacks mtDNA was so remarkable. Here, by reanalyzing recently published genomic and transcriptomic data from three Amoebophrya strains, we provide evidence of a cryptic, highly reduced mtDNA in this clade. More work is needed before one can definitively say if Amoebophrya has or does not have an mtDNA, but for now, the data are pointing toward the existence of one. Ultimately, we urge caution when basing supposedly absent genomic features on single line evidences.
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Affiliation(s)
- Ehsan Kayal
- Fédération de Recherche 2424 Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, Roscoff, France
| | - David R Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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42
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Wagner AO, Westerholm M, Stres B, Kopečný J. Editorial: Exploring the Role and Function of the Microbiota in Terrestrial Anaerobic Environments and Their Potential Biotechnological Application. Front Microbiol 2021; 12:722268. [PMID: 34385996 PMCID: PMC8353394 DOI: 10.3389/fmicb.2021.722268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Maria Westerholm
- Department of Molecular Sciences, BioCentre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Blaz Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
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43
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Slobodkina G, Allioux M, Merkel A, Cambon-Bonavita MA, Alain K, Jebbar M, Slobodkin A. Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus. Front Microbiol 2021; 12:679245. [PMID: 34335500 PMCID: PMC8322695 DOI: 10.3389/fmicb.2021.679245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022] Open
Abstract
Hyperthermophilic archaea of the genus Archaeoglobus are the subject of many fundamental and biotechnological researches. Despite their significance, the class Archaeoglobi is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of Archaeoglobus from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name Archaeoglobus neptunius sp. nov. is proposed. The type strain is SE56T (=DSM 110954T = VKM B-3474T). The cells of the novel isolate are motile irregular cocci growing at 50–85°C, pH 5.5–7.5, and NaCl concentrations of 1.5–4.5% (w/v). Strain SE56T grows lithoautotrophically with H2 as an electron donor, sulfite or thiosulfate as an electron acceptor, and CO2/HCO3− as a carbon source. It is also capable of chemoorganotrophic growth by reduction of sulfate, sulfite, or thiosulfate. The genome of the new isolate consists of a 2,115,826 bp chromosome with an overall G + C content of 46.0 mol%. The whole-genome annotation confirms the key metabolic features of the novel isolate demonstrated experimentally. Genome contains a complete set of genes involved in CO2 fixation via reductive acetyl-CoA pathway, gluconeogenesis, hydrogen and fatty acids oxidation, sulfate reduction, and flagellar motility. The phylogenomic reconstruction based on 122 conserved single-copy archaeal proteins supported by average nucleotide identity (ANI), average amino acid identity (AAI), and alignment fraction (AF) values, indicates a polyphyletic origin of the species currently included into the genus Archaeoglobus, warranting its reclassification.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marie-Anne Cambon-Bonavita
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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44
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Wang C, Dang T, Baste J, Anil Joshi A, Bhushan A. A novel standalone microfluidic device for local control of oxygen tension for intestinal-bacteria interactions. FASEB J 2021; 35:e21291. [PMID: 33506497 DOI: 10.1096/fj.202001600rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
The intestinal environment is unique because it supports the intestinal epithelial cells under a normal oxygen environment and the microbiota under an anoxic environment. Due to importance of understanding the interactions between the epithelium and the microbiota, there is a strong need for developing representative and simple experimental models. Current approaches do not capture the partitioned oxygen environment, require external anaerobic chambers, or are complex. Another major limitation is that with the solutions that can mimic this oxygen environment, the oxygenation level of the epithelial cells is not known, raising the question whether the cells are hypoxic or not. We report standalone microfluidic devices that form a partitioned oxygen environment without the use of an external anaerobic chamber or oxygen scavengers to coculture intestinal epithelial and bacterial cells. By changing the thickness of the device cover, the oxygen tension in the chamber was modulated. We verified the oxygen levels using several tests: microscale oxygen sensitive sensors which were integrated within the devices, immunostaining of Caco-2 cells to determine hypoxia levels, and genetically encoded bacteria to visualize the growth. Collectively, these methods monitored oxygen concentrations in the devices more comprehensively than previous reports and allowed for control of oxygen tension to match the requirements of both intestinal cells and anaerobic bacteria. Our experimental model is supported by the mathematical model that considered diffusion of oxygen into the top chamber. This allowed us to experimentally determine the oxygen consumption rate of the intestinal epithelial cells under perfusion.
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Affiliation(s)
- Chengyao Wang
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Thao Dang
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Jasmine Baste
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Advait Anil Joshi
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
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45
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Huang F, Sardari RRR, Jasilionis A, Böök O, Öste R, Rascón A, Heyman‐Lindén L, Holst O, Karlsson EN. Cultivation of the gut bacterium Prevotella copri DSM 18205 T using glucose and xylose as carbon sources. Microbiologyopen 2021; 10:e1213. [PMID: 34180602 PMCID: PMC8236902 DOI: 10.1002/mbo3.1213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Prevotella copri DSM18205T is a human gut bacterium, suggested as a next-generation probiotic. To utilize it as such, it is, however, necessary to grow the species in a reproducible manner. Prevotella copri has previously been reported to be highly sensitive to oxygen, and hence difficult to isolate and cultivate. This study presents successful batch cultivation strategies for viable strain inoculations and growth in both serum bottles and a stirred tank bioreactor (STR), without the use of an anaerobic chamber, as long as the cells were kept in the exponential growth phase. A low headspace volume in the STR was important to reach high cell density. P. copri utilized xylose cultivated in Peptone Yeast Xylose medium (PYX medium), resulting in a comparable growth rate and metabolite production as in Peptone Yeast Glucose medium (PYG medium) in batch cultivations at pH 7.2.Up to 5 g/L of the carbon source was consumed, leading to the production of succinic acid, acetic acid, and formic acid, and cell densities (OD620 nm ) in the range 6-7.5. The highest yield of produced succinic acid was 0.63 ± 0.05 g/g glucose in PYG medium cultivations and 0.88 ± 0.06 g/g xylose in PYX medium cultivations.
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Affiliation(s)
- Fang Huang
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
- Aventure ABLundSweden
| | - Roya R. R. Sardari
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
| | - Andrius Jasilionis
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
| | | | | | - Ana Rascón
- Department of Food Technology, Engineering and NutritionLund UniversityLundSweden
| | | | - Olle Holst
- Division of BiotechnologyDepartment of ChemistryLund UniversityLundSweden
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46
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Susanti D, Frazier MC, Mukhopadhyay B. Corrigendum: A Genetic System for Methanocaldococcus jannaschii: An Evolutionary Deeply Rooted Hyperthermophilic Methanarchaeon. Front Microbiol 2021; 12:649127. [PMID: 33767687 PMCID: PMC7986713 DOI: 10.3389/fmicb.2021.649127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Mary C Frazier
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
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47
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Ochi K, Tokuda M, Yanagiya K, Suzuki-Minakuchi C, Nojiri H, Yuki M, Ohkuma M, Kimbara K, Shintani M. Oxygen concentration affects frequency and range of transconjugants for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1. Biosci Biotechnol Biochem 2021; 85:1005-1015. [PMID: 33580688 DOI: 10.1093/bbb/zbaa118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/20/2020] [Indexed: 11/12/2022]
Abstract
The frequency of transconjugants were compared for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1 under aerobic and anaerobic conditions. Filter mating assays were performed with one donor strain and one recipient strain using different donors of Pseudomonas and recipient strains, including Pseudomonas, Pantoea, and Buttiauxella. Under anaerobic condition, frequencies of transconjugants for both plasmids were 101-103-fold lower than those under aerobic condition regardless of whether aerobically or anaerobically grown donors and recipients were used. To compare the transconjugant ranges under aerobic and anaerobic conditions, conjugation was performed between the donor of pBP136 and recipient bacteria extracted from environmental samples. Several transconjugants were uniquely obtained from each aerobic or anaerobic condition. Our findings indicate that a plasmid can differently spread among bacteria depending on the oxygen concentrations of the environment.
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Affiliation(s)
- Kentaro Ochi
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Maho Tokuda
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kosuke Yanagiya
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
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Pricop GR, Gheorghe I, Pircalabioru GG, Cristea V, Popa M, Marutescu L, Chifiriuc MC, Mihaescu G, Bezirtzoglou E. Resistance and Virulence Features of Bacteroides spp. Isolated from Abdominal Infections in Romanian Patients. Pathogens 2020; 9:pathogens9110940. [PMID: 33198093 PMCID: PMC7696418 DOI: 10.3390/pathogens9110940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Anaerobic bacteria are predominant residents of the normal microbiota of the skin and mucous membranes but are also known to be associated with a number of human infections including peritonitis, appendicitis, abscesses, ulcers and wound infections. Herein, we investigate the antibiotic resistance profiles as well as the genetic support of antibiotic resistance and virulence determinants of anaerobic bacteria isolated from intra-abdominal infections. The study was performed on 198 Romanian patients from which different clinical samples were taken intra-operatory and sent for microbiological analyses. From the total number of isolated strains, a subset of 75 Bacteroides spp. were selected and further investigated for antibiotic resistance and virulence features, at phenotypic and genetic level. Our results obtained through the analysis of a significant number of Bacteroides strains could shed light on the virulence potential and mechanisms by which anaerobic bacteria can cause endogenous infections.
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Affiliation(s)
- Gabriela Roxana Pricop
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
| | - Irina Gheorghe
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
- Department of Earth, Environment and Life Sciences, The Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania;
- Correspondence: (I.G.); (G.G.P.)
| | - Gratiela Gradisteanu Pircalabioru
- Department of Earth, Environment and Life Sciences, The Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania;
- Correspondence: (I.G.); (G.G.P.)
| | - Violeta Cristea
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
| | - Marcela Popa
- Department of Earth, Environment and Life Sciences, The Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania;
| | - Luminita Marutescu
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
- Department of Earth, Environment and Life Sciences, The Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
- Department of Earth, Environment and Life Sciences, The Research Institute of the University of Bucharest (ICUB), University of Bucharest, 050095 Bucharest, Romania;
- Academy of Romanian Scientists, 050045 Bucharest, Romania
| | - Grigore Mihaescu
- Faculty of Biology, Department of Microbiology and Immunology, University of Bucharest, 060101 Bucharest, Romania; (G.R.P.); (V.C.); (L.M.); (M.C.C.); (G.M.)
| | - Eugenia Bezirtzoglou
- Laboratory of Microbiology, Biotechnology and Hygiene, Department of Food Science and Technology, Faculty of Agricultural Development, Democritus University of Thrace, 67100 Orestiada, Greece;
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Gajdács M, Urbán E. The Pathogenic Role of Actinomyces spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era. Antibiotics (Basel) 2020; 9:E524. [PMID: 32824418 PMCID: PMC7459602 DOI: 10.3390/antibiotics9080524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases-with a special focus on newly described species-in particular their role in genitourinary tract infections in females and males.
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Affiliation(s)
- Márió Gajdács
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, 6720 Szeged, Hungary;
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Edit Urbán
- Institute of Translational Medicine, Faculty of Medicine, University of Pécs, 7624 Pécs, Hungary
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Begum K, Bassères E, Miranda J, Lancaster C, Gonzales-Luna AJ, Carlson TJ, Rashid T, Eyre DW, Wilcox MH, Alam MJ, Garey KW. In Vitro Activity of Omadacycline, a New Tetracycline Analog, and Comparators against Clostridioides difficile. Antimicrob Agents Chemother 2020; 64:e00522-20. [PMID: 32513796 DOI: 10.1128/AAC.00522-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/31/2020] [Indexed: 02/06/2023] Open
Abstract
Omadacycline is a potent aminomethylcycline with in vitro activity against Gram-positive, Gram-negative, and anaerobic bacteria. Preliminary data demonstrated that omadacycline has in vitro activity against Clostridioides difficile; however, large-scale in vitro studies have not been done. The purpose of this study was to assess the in vitro susceptibility of omadacycline and comparators on a large biobank of clinical C. difficile isolates. Omadacycline is a potent aminomethylcycline with in vitro activity against Gram-positive, Gram-negative, and anaerobic bacteria. Preliminary data demonstrated that omadacycline has in vitro activity against Clostridioides difficile; however, large-scale in vitro studies have not been done. The purpose of this study was to assess the in vitro susceptibility of omadacycline and comparators on a large biobank of clinical C. difficile isolates. In vitroC. difficile susceptibility to omadacycline and comparators (fidaxomicin, metronidazole, and vancomycin) was assessed using the broth microdilution method. Minimum bactericidal concentrations (MBCs) and time-kill assays were assessed for pharmacodynamics analysis, and whole-genome sequencing was performed in a subset of isolates to assess distribution of MICs and resistance determinants. Two hundred fifty clinical C. difficile isolates collected between 2015 and 2018 were tested for in vitro susceptibility of omadacycline and comparators. Ribotypes included F001 (n = 5), F002 (n = 56), F014-020 (n = 66), F017 (n = 8), F027 (n = 53), F106 (n = 45), and F255 (n = 17). Omadacycline demonstrated potent in vitro activity with an MIC range of 0.016 to 0.13 μg/ml, an MIC50 of 0.031 μg/ml, and an MIC90 of 0.031 μg/ml. No difference was observed for omadacycline MIC50 and MIC90 values stratified by ribotype, disease severity, or vancomycin susceptibility. Bactericidal activity was confirmed in time-kill studies. No difference was observed in MIC based on C. difficile phylogeny. Further development of omadacycline as an intravenous and oral antibiotic directed toward C. difficile infection is warranted.
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