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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Djemai K, Gouriet F, Michel J, Radulesco T, Drancourt M, Grine G. Methanobrevibacter smithii tonsillar phlegmon: a case report. New Microbes New Infect 2021; 42:100891. [PMID: 34141438 PMCID: PMC8184653 DOI: 10.1016/j.nmni.2021.100891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Untreated tonsillar phlegmon is a life-threatening condition commonly caused by Streptococcus pyogenes and Fusobacterium necrophorum, among other pathogens. Here, using specific laboratory tools, we detected Methanobrevibacter smithii in addition to S. pyogenes. This unprecedented observation questions the role of methanogens in phlegmon and the optimal treatment of this mixed infection.
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Affiliation(s)
- K Djemai
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - F Gouriet
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - J Michel
- CHU Hôpital de la Conception, Service ORL et Chirurgie cervico-faciale, Marseille, France
| | - T Radulesco
- CHU Hôpital de la Conception, Service ORL et Chirurgie cervico-faciale, Marseille, France
| | - M Drancourt
- Aix-Marseille Univ, IRD, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - G Grine
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, UFR Odontologie, Marseille, France
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Guindo CO, Drancourt M, Grine G. Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens. Microb Pathog 2020; 149:104425. [PMID: 32745665 DOI: 10.1016/j.micpath.2020.104425] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.
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Affiliation(s)
- C O Guindo
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - M Drancourt
- IHU Méditerranée Infection, Marseille, France
| | - G Grine
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, UFR Odontologie, Marseille, France.
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Grine G, Lotte R, Chirio D, Chevalier A, Raoult D, Drancourt M, Ruimy R. Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection. EBioMedicine 2019; 43:333-337. [PMID: 31072770 PMCID: PMC6558020 DOI: 10.1016/j.ebiom.2019.04.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/10/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context. METHODS In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI). FINDINGS Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis. INTERPRETATION Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. FUND: This study was supported by IHU Méditerranée Infection, Marseille, France.
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Affiliation(s)
- Ghiles Grine
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France
| | - Romain Lotte
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France; Inserm U1065, C3M, Equipe 6 « Virulence microbienne et signalisation inflammatoire », Bâtiment universitaire Archimède, Nice, France
| | - David Chirio
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet I, Nice, France
| | - Alicia Chevalier
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France
| | - Didier Raoult
- Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Raymond Ruimy
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l'Archet II, Nice, France; Université Côte d'Azur, Inserm, C3M, Nice, France; Inserm U1065, C3M, Equipe 6 « Virulence microbienne et signalisation inflammatoire », Bâtiment universitaire Archimède, Nice, France.
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Sogodogo E, Drancourt M, Grine G. Methanogens as emerging pathogens in anaerobic abscesses. Eur J Clin Microbiol Infect Dis 2019; 38:811-818. [DOI: 10.1007/s10096-019-03510-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 01/02/2023]
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Guilhot E, Khelaifia S, La Scola B, Raoult D, Dubourg G. Methods for culturing anaerobes from human specimen. Future Microbiol 2018; 13:369-381. [PMID: 29446650 DOI: 10.2217/fmb-2017-0170] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Anaerobes represent the dominating population in the human gut microbiota and play a key role in gut homeostasis. In addition, several anaerobes are now considered as probiotics and they remain essential to several processes in the field of biotechnology. With the implementation of MALDI-TOF MS in routine laboratories, anaerobes are no longer neglected in clinical microbiology, as their identification is made easy. However, the isolation and identification of anaerobic bacteria, remains time consuming, fastidious and costly. Various strategies have been developed, from sampling to culturing human specimens, which will be discussed in this paper. Also, particular attention is paid to isolating species with special medical importance, as for contribution to the field of culturomics.
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Affiliation(s)
- Elodie Guilhot
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
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Drancourt M, Nkamga VD, Lakhe NA, Régis JM, Dufour H, Fournier PE, Bechah Y, Michael Scheld W, Raoult D. Evidence of Archaeal Methanogens in Brain Abscess. Clin Infect Dis 2017; 65:1-5. [DOI: 10.1093/cid/cix286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/28/2017] [Indexed: 11/13/2022] Open
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Demonfort Nkamga V, Armstrong N, Drancourt M. In vitro susceptibility of cultured human methanogens to lovastatin. Int J Antimicrob Agents 2016; 49:176-182. [PMID: 27955920 DOI: 10.1016/j.ijantimicag.2016.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 11/29/2022]
Abstract
Lovastatin is a prodrug that is hydrolysed in vivo to β-hydroxy acid lovastatin, which inhibits 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-Co-A) reductase (HMGR), thereby lowering cholesterol in humans. A side effect of lovastatin is inhibition of isoprenoid synthesis and cell membrane formation in methanogenic Archaea, which are members of the human digestive tract microbiota and are emerging pathogens. In this study, the in vitro susceptibility of the human-associated methanogens Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter massiliense, Methanobrevibacter arboriphilus and Methanomassiliicoccus luminyensis to lovastatin (1-4 µg/mL) was tested in the presence of five gut anaerobes aiming to metabolise lovastatin into β-hydroxy acid lovastatin as confirmed by ultra-high-performance liquid chromatography. Five days of incubation with lovastatin had no measurable effect on the growth of the five gut anaerobes but significantly reduced CH4 production and methanogen growth as measured by quantitative PCR (P <0.01). Quantitative PCR analyses indicated that compared with controls, β-hydroxy acid lovastatin significantly increased the expression of the genes mta and mcrA implicated in methanogenesis and significantly decreased the expression of the fno gene implicated in methanogenesis. Expression of the HMGR gene (hmg) implicated in cell wall synthesis was significantly increased by β-hydroxy acid lovastatin (P <0.01). These results strongly suggest that in the presence of gut anaerobes, lovastatin yields β-hydroxy acid lovastatin, which inhibits methane production and growth of methanogens by affecting their cell membrane biosynthesis. Lovastatin is the first licensed drug to exclusively affect the growth of methanogens whilst protecting the bacterial microbiota.
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Affiliation(s)
- Vanessa Demonfort Nkamga
- Aix-Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, Marseille 13005, France
| | - Nicholas Armstrong
- Aix-Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, Marseille 13005, France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, Marseille 13005, France.
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Nkamga VD, Lotte R, Roger PM, Drancourt M, Ruimy R. Methanobrevibacter smithii and Bacteroides thetaiotaomicron cultivated from a chronic paravertebral muscle abscess. Clin Microbiol Infect 2016; 22:1008-1009. [PMID: 27664777 DOI: 10.1016/j.cmi.2016.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 12/11/2022]
Affiliation(s)
- V D Nkamga
- Unité de recherche sur les maladies infectieuses tropicales et émergentes, Marseille, France
| | - R Lotte
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Nice, France; Université de Nice Côte d'azur, Faculté de Médecine, Nice, France; Inserm U1065, C3M, Team6, 'Bacterial toxins in host pathogen interactions', Bâtiment universitaire Archimed, Nice, France
| | - P-M Roger
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire de Nice, Nice, France
| | - M Drancourt
- Unité de recherche sur les maladies infectieuses tropicales et émergentes, Marseille, France
| | - R Ruimy
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Nice, Nice, France; Université de Nice Côte d'azur, Faculté de Médecine, Nice, France; Inserm U1065, C3M, Team6, 'Bacterial toxins in host pathogen interactions', Bâtiment universitaire Archimed, Nice, France.
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Muskal SM, Sliman J, Kokai-Kun J, Pimentel M, Wacher V, Gottlieb K. Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway. F1000Res 2016; 5:606. [PMID: 27347377 PMCID: PMC4909102 DOI: 10.12688/f1000research.8406.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 12/14/2023] Open
Abstract
UNLABELLED Methane produced by the methanoarchaeon Methanobrevibacter smithii ( M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings. METHODS F420-dependent methylenetetrahydromethanopterin dehydrogenase ( mtd), a key methanogenesis enzyme was modeled for two different methanogenic archaea: M. smithii and Methanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures. RESULTS 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial ( NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo. CONCLUSION The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligand in silico and thus could inhibit the activity of the key M. smithii methanogenesis enzyme mtd in vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.
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Muskal SM, Sliman J, Kokai-Kun J, Pimentel M, Wacher V, Gottlieb K. Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway. F1000Res 2016; 5:606. [PMID: 27347377 PMCID: PMC4909102 DOI: 10.12688/f1000research.8406.3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2016] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED Methane produced by the methanoarchaeon Methanobrevibacter smithii ( M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings. METHODS F420-dependent methylenetetrahydromethanopterin dehydrogenase ( mtd), a key methanogenesis enzyme was modeled for two different methanogenic archaea: M. smithii and Methanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures. RESULTS 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial ( NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo. CONCLUSION The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligand in silico and thus could inhibit the activity of the key M. smithii methanogenesis enzyme mtd in vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.
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12
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Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis 2016; 35:985-91. [DOI: 10.1007/s10096-016-2627-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/13/2016] [Indexed: 11/26/2022]
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13
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Gottlieb K, Wacher V, Sliman J, Pimentel M. Review article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders. Aliment Pharmacol Ther 2016; 43:197-212. [PMID: 26559904 PMCID: PMC4737270 DOI: 10.1111/apt.13469] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 09/29/2015] [Accepted: 10/20/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Observational studies show a strong association between delayed intestinal transit and the production of methane. Experimental data suggest a direct inhibitory activity of methane on the colonic and ileal smooth muscle and a possible role for methane as a gasotransmitter. Archaea are the only confirmed biological sources of methane in nature and Methanobrevibacter smithii is the predominant methanogen in the human intestine. AIM To review the biosynthesis and composition of archaeal cell membranes, archaeal methanogenesis and the mechanism of action of statins in this context. METHODS Narrative review of the literature. RESULTS Statins can inhibit archaeal cell membrane biosynthesis without affecting bacterial numbers as demonstrated in livestock and humans. This opens the possibility of a therapeutic intervention that targets a specific aetiological factor of constipation while protecting the intestinal microbiome. While it is generally believed that statins inhibit methane production via their effect on cell membrane biosynthesis, mediated by inhibition of the HMG-CoA reductase, there is accumulating evidence for an alternative or additional mechanism of action where statins inhibit methanogenesis directly. It appears that this other mechanism may predominate when the lactone form of statins, particularly lovastatin lactone, is administered. CONCLUSIONS Clinical development appears promising. A phase 2 clinical trial is currently in progress that evaluates the effect of lovastatin lactone on methanogenesis and symptoms in patients with irritable bowel syndrome with constipation. The review concludes with an outlook for the future and subsequent work that needs to be done.
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Affiliation(s)
| | - V. Wacher
- Synthetic BiologicsInc.RockvilleMDUSA
| | - J. Sliman
- Synthetic BiologicsInc.RockvilleMDUSA
| | - M. Pimentel
- GastroenterologyCedars‐Sinai Medical CenterLos AngelesCAUSA
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Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev 2015; 28:208-36. [PMID: 25567228 DOI: 10.1128/cmr.00110-14] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.
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