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Patra AK, Puchala R. Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways. Biotechnol Adv 2023; 69:108268. [PMID: 37793598 DOI: 10.1016/j.biotechadv.2023.108268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.
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Affiliation(s)
- Amlan Kumar Patra
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA.
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; Applied Physiology Unit, Military Institute of Hygiene and Epidemiology, Kozielska 4, Warsaw, Poland
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Napolitano M, Fasulo E, Ungaro F, Massimino L, Sinagra E, Danese S, Mandarino FV. Gut Dysbiosis in Irritable Bowel Syndrome: A Narrative Review on Correlation with Disease Subtypes and Novel Therapeutic Implications. Microorganisms 2023; 11:2369. [PMID: 37894027 PMCID: PMC10609453 DOI: 10.3390/microorganisms11102369] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disorder characterized by chronic abdominal pain and altered bowel habits. It can be subclassified in different subtypes according to the main clinical manifestation: constipation, diarrhea, mixed, and unclassified. Over the past decade, the role of gut microbiota in IBS has garnered significant attention in the scientific community. Emerging research spotlights the intricate involvement of microbiota dysbiosis in IBS pathogenesis. Studies have demonstrated reduced microbial diversity and stability and specific microbial alterations for each disease subgroup. Microbiota-targeted treatments, such as antibiotics, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and even diet, offer exciting prospects for managing IBS. However, definitive conclusions are hindered by the heterogeneity of these studies. Further research should focus on elucidating the mechanisms, developing microbiome-based diagnostics, and enabling personalized therapies tailored to an individual's microbiome profile. This review takes a deep dive into the microscopic world inhabiting our guts, and its implications for IBS. Our aim is to elucidate the complex interplay between gut microbiota and each IBS subtype, exploring novel microbiota-targeted treatments and providing a comprehensive overview of the current state of knowledge.
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Affiliation(s)
- Maria Napolitano
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Ernesto Fasulo
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Federica Ungaro
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Luca Massimino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy;
| | - Silvio Danese
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Gastroenterology and Endoscopy, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesco Vito Mandarino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
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Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. Methanogenic archaea in the human gastrointestinal tract. Nat Rev Gastroenterol Hepatol 2022; 19:805-813. [PMID: 36050385 DOI: 10.1038/s41575-022-00673-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 12/24/2022]
Abstract
The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.
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Affiliation(s)
- Christoph Hoegenauer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heinz F Hammer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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Methanogens and Hydrogen Sulfide Producing Bacteria Guide Distinct Gut Microbe Profiles and Irritable Bowel Syndrome Subtypes. Am J Gastroenterol 2022; 117:2055-2066. [PMID: 36114762 PMCID: PMC9722381 DOI: 10.14309/ajg.0000000000001997] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Irritable bowel syndrome (IBS) includes diarrhea-predominant (IBS-D) and constipation-predominant (IBS-C) subtypes. We combined breath testing and stool microbiome sequencing to identify potential microbial drivers of IBS subtypes. METHODS IBS-C and IBS-D subjects from 2 randomized controlled trials (NCT03763175 and NCT04557215) were included. Baseline breath carbon dioxide, hydrogen (H 2 ), methane (CH 4 ), and hydrogen sulfide (H 2 S) levels were measured by gas chromatography, and baseline stool microbiome composition was analyzed by 16S rRNA sequencing. Microbial metabolic pathways were analyzed using Kyoto Encyclopedia of Genes and Genomes collection databases. RESULTS IBS-C subjects had higher breath CH 4 that correlated with higher gut microbial diversity and higher relative abundance (RA) of stool methanogens, predominantly Methanobrevibacter , as well as higher absolute abundance of Methanobrevibacter smithii in stool. IBS-D subjects had higher breath H 2 that correlated with lower microbial diversity and higher breath H 2 S that correlated with higher RA of H 2 S-producing bacteria, including Fusobacterium and Desulfovibrio spp. The predominant H 2 producers were different in these distinct microtypes, with higher RA of Ruminococcaceae and Christensenellaceae in IBS-C/CH 4 + (which correlated with Methanobacteriaceae RA) and higher Enterobacteriaceae RA in IBS-D. Finally, microbial metabolic pathway analysis revealed enrichment of Kyoto Encyclopedia of Genes and Genomes modules associated with methanogenesis and biosynthesis of methanogenesis cofactor F420 in IBS-C/CH 4 + subjects, whereas modules associated with H 2 S production, including sulfate reduction pathways, were enriched in IBS-D. DISCUSSION Our findings identify distinct gut microtypes linked to breath gas patterns in IBS-C and IBS-D subjects, driven by methanogens such as M. smithii and H 2 S producers such as Fusobacterium and Desulfovibrio spp, respectively.
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Khan MZ, Lyu R, McMichael J, Gabbard S. Chronic Intestinal Pseudo-Obstruction Is Associated with Intestinal Methanogen Overgrowth. Dig Dis Sci 2022; 67:4834-4840. [PMID: 35001241 DOI: 10.1007/s10620-021-07343-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Chronic intestinal pseudo-obstruction (CIP) is a rare motility disorder characterized by dilated small bowel in the absence of mechanical obstruction. CIP has a known association with small intestinal bacterial overgrowth (SIBO); however, data regarding association with specific subtypes such as methane-positive (M+) and hydrogen-positive (H+) SIBO are limited. Therefore, we conducted this study to characterize subtypes of SIBO in CIP and compare them with non-CIP patients. AIMS The aim is to explore the association and prevalence of hydrogen and methane subtypes of SIBO in patients with CIP. METHODS A retrospective chart review was conducted for 494 patients who underwent glucose breath tests (GBT) in 2019. CIP was diagnosed based on clinical suspicion and after ruling out mechanical obstruction. We also reviewed demographic data, including age, gender, body mass index, tobacco and alcohol history, medical comorbidities, use of proton pump inhibitors, and history of colectomy. RESULTS Among 494 patients, 7.7% (38) had CIP. The prevalence of M+ GBT in CIP patients was higher compared with non-CIP patients, and it was significant [52.6% (20/38) versus 11.8% (54/456), p < 0.001]. The prevalence of H+ GBT in our cohort of CIP patients was similar to that of non-CIP patients [23.7% (9/38) versus 25.7% (117/456), p = 0.941]. CONCLUSION The prevalence of methane-positive GBT was higher in CIP patients than in patients without CIP. This finding further strengthens the hypothesis that the relationship between motility disorders and methanogen overgrowth is facilitative.
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Affiliation(s)
| | - Ruishen Lyu
- Department of Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - John McMichael
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Scott Gabbard
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, OH, USA
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Gut Non-Bacterial Microbiota: Emerging Link to Irritable Bowel Syndrome. Toxins (Basel) 2022; 14:toxins14090596. [PMID: 36136534 PMCID: PMC9503233 DOI: 10.3390/toxins14090596] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022] Open
Abstract
As a common functional gastrointestinal disorder, irritable bowel syndrome (IBS) significantly affects personal health and imposes a substantial economic burden on society, but the current understanding of its occurrence and treatment is still inadequate. Emerging evidence suggests that IBS is associated with gut microbial dysbiosis, but most studies focus on the bacteria and neglect other communities of the microbiota, including fungi, viruses, archaea, and other parasitic microorganisms. This review summarizes the latest findings that link the nonbacterial microbiota with IBS. IBS patients show less fungal and viral diversity but some alterations in mycobiome, virome, and archaeome, such as an increased abundance of Candida albicans. Moreover, fungi and methanogens can aid in diagnosis. Fungi are related to distinct IBS symptoms and induce immune responses, intestinal barrier disruption, and visceral hypersensitivity via specific receptors, cells, and metabolites. Novel therapeutic methods for IBS include fungicides, inhibitors targeting fungal pathogenic pathways, probiotic fungi, prebiotics, and fecal microbiota transplantation. Additionally, viruses, methanogens, and parasitic microorganisms are also involved in the pathophysiology and treatment. Therefore, the gut nonbacterial microbiota is involved in the pathogenesis of IBS, which provides a novel perspective on the noninvasive diagnosis and precise treatment of this disease.
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Djemai K, Drancourt M, Tidjani Alou M. Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions. MICROBIAL ECOLOGY 2022; 83:536-554. [PMID: 34169332 DOI: 10.1007/s00248-021-01796-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.
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Affiliation(s)
- Kenza Djemai
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Maryam Tidjani Alou
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France.
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Ábrego-Gacía A, Poggi-Varaldo HM, Robles-González V, Ponce-Noyola T, Calva-Calva G, Ríos-Leal E, Estrada-Bárcenas D, Mendoza-Vargas A. Lovastatin as a supplement to mitigate rumen methanogenesis: an overview. J Anim Sci Biotechnol 2021; 12:123. [PMID: 34911584 PMCID: PMC8675506 DOI: 10.1186/s40104-021-00641-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/03/2021] [Indexed: 11/23/2022] Open
Abstract
Methane from enteric fermentation is the gas with the greatest environmental impact emitted by ruminants. Lovastatin (Lv) addition to feedstocks could be a strategy to mitigate rumen methane emissions via decreasing the population of methanogenic archaea (MA). Thus, this paper provides the first overview of the effects of Lv supplementation, focusing on the inhibition of methane production, rumen microbiota, and ruminal fermentation. Results indicated that Lv treatment had a strong anti-methanogenic effect on pure strains of MA. However, there are uncertainties from in vitro rumen fermentation trials with complex substrates and rumen inoculum. Solid-state fermentation (SSF) has emerged as a cost-effective option to produce Lv. In this way, SSF of agricultural residues as an Lv-carrier supplement in sheep and goats demonstrated a consistent decrease in ruminal methane emissions. The experimental evidence for in vitro conditions showed that Lv did not affect the volatile fatty acids (VFA). However, in vivo experiments demonstrated that the production of VFA was decreased. Lv did not negatively affect the digestibility of dry matter during in vitro and in vivo methods, and there is even evidence that it can induce an increase in digestibility. Regarding the rumen microbiota, populations of MA were reduced, and no differences were detected in alpha and beta diversity associated with Lv treatment. However, some changes in the relative abundance of the microbiota were induced. Further studies are recommended on: (i) Lv biodegradation products and stability, as well as its adsorption onto the solid matter in the rumen, to gain more insight on the “available” or effective Lv concentration; and (ii) to determine whether the effect of Lv on ruminal fermentation also depends on the feed composition and different ruminants.
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Affiliation(s)
- Amaury Ábrego-Gacía
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Héctor M Poggi-Varaldo
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico. .,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.
| | - Vania Robles-González
- Instituto de Hidrología, Universidad Tecnológica de la Mixteca, Oaxaca, 69000, Huajuapan de León, Mexico
| | - Teresa Ponce-Noyola
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Graciano Calva-Calva
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Elvira Ríos-Leal
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Daniel Estrada-Bárcenas
- National Collection of Microbial and Cellular Cultures, CINVESTAV-IPN, P.O.Box17-740, 07000, Mexico City, Mexico
| | - Alfredo Mendoza-Vargas
- Unidad de Secuenciación e Identificación de Polimorfismos, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
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Shabanzadeh AP, Charish J, Tassew NG, Farhani N, Feng J, Qin X, Sugita S, Mothe AJ, Wälchli T, Koeberle PD, Monnier PP. Cholesterol synthesis inhibition promotes axonal regeneration in the injured central nervous system. Neurobiol Dis 2021; 150:105259. [PMID: 33434618 DOI: 10.1016/j.nbd.2021.105259] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/24/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Neuronal regeneration in the injured central nervous system is hampered by multiple extracellular proteins. These proteins exert their inhibitory action through interactions with receptors that are located in cholesterol rich compartments of the membrane termed lipid rafts. Here we show that cholesterol-synthesis inhibition prevents the association of the Neogenin receptor with lipid rafts. Furthermore, we show that cholesterol-synthesis inhibition enhances axonal growth both on inhibitory -myelin and -RGMa substrates. Following optic nerve injury, lowering cholesterol synthesis with both drugs and siRNA-strategies allows for robust axonal regeneration and promotes neuronal survival. Cholesterol inhibition also enhanced photoreceptor survival in a model of Retinitis Pigmentosa. Our data reveal that Lovastatin leads to several opposing effects on regenerating axons: cholesterol synthesis inhibition promotes regeneration whereas altered prenylation impairs regeneration. We also show that the lactone prodrug form of lovastatin has differing effects on regeneration when compared to the ring-open hydroxy-acid form. Thus the association of cell surface receptors with lipid rafts contributes to axonal regeneration inhibition, and blocking cholesterol synthesis provides a potential therapeutic approach to promote neuronal regeneration and survival in the diseased Central Nervous System. SIGNIFICANCE STATEMENT: Statins have been intensively used to treat high levels of cholesterol in humans. However, the effect of cholesterol inhibition in both the healthy and the diseased brain remains controversial. In particular, it is unclear whether cholesterol inhibition with statins can promote regeneration and survival following injuries. Here we show that late stage cholesterol inhibition promotes robust axonal regeneration following optic nerve injury. We identified distinct mechanisms of action for activated vs non-activated Lovastatin that may account for discrepancies found in the literature. We show that late stage cholesterol synthesis inhibition alters Neogenin association with lipid rafts, thereby i) neutralizing the inhibitory function of its ligand and ii) offering a novel opportunity to promote CNS regeneration and survival following injuries.
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Affiliation(s)
- Alireza P Shabanzadeh
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Physiology, Donald K. Johnson Research Institute, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Anatomy, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Jason Charish
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Physiology, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Nardos G Tassew
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Physiology, Donald K. Johnson Research Institute, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada
| | - Nahal Farhani
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada
| | - Jinzhou Feng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xinjue Qin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shuzo Sugita
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada
| | - Andrea J Mothe
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada
| | - Thomas Wälchli
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada
| | - Paulo D Koeberle
- Department of Anatomy, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Philippe P Monnier
- Krembil Research Institute, KDT 8-417, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Physiology, Donald K. Johnson Research Institute, 60 Leonard St., Toronto M5T 2S8, Ontario, Canada; Department of Ophthalmology, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada; Department of Physiology, Faculty of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada.
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10
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Cuccioloni M, Bonfili L, Cecarini V, Cocchioni F, Petrelli D, Crotti E, Zanchi R, Eleuteri AM, Angeletti M. Structure/activity virtual screening and in vitro testing of small molecule inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from gut methanogenic bacteria. Sci Rep 2020; 10:13150. [PMID: 32753591 PMCID: PMC7588429 DOI: 10.1038/s41598-020-70042-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Virtual screening techniques and in vitro binding/inhibitory assays were used to search within a set of more than 8,000 naturally occurring small ligands for candidate inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase (FNO) from Methanobrevibacter smithii, the enzyme that catalyses the bidirectional electron transfer between NADP+ and F420H2 during the intestinal production of CH4 from CO2. In silico screening using molecular docking classified the ligand-enzyme complexes in the range between - 4.9 and - 10.5 kcal/mol. Molecular flexibility, the number of H-bond acceptors and donors, the extent of hydrophobic interactions, and the exposure to the solvent were the major discriminants in determining the affinity of the ligands for FNO. In vitro studies on a group of these ligands selected from the most populated/representative clusters provided quantitative kinetic, equilibrium, and structural information on ligands' behaviour, in optimal agreement with the predictive computational results.
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Affiliation(s)
- Massimiliano Cuccioloni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
| | - Laura Bonfili
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Valentina Cecarini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Filippo Cocchioni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Dezemona Petrelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133, Milan, Italy
| | - Raffaella Zanchi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133, Milan, Italy
| | - Anna Maria Eleuteri
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Mauro Angeletti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
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Niewinna K, Zielińska A, Fichna J. Recent advances in the pharmacological management of constipation predominant irritable bowel syndrome. Expert Opin Pharmacother 2019; 21:73-84. [PMID: 31724881 DOI: 10.1080/14656566.2019.1688784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Irritable bowel syndrome (IBS) is a complex functional gut disorder that typically manifests in early adult years. More than a third of IBS patients are diagnosed with predominant constipation subtype (IBS-C). This syndrome has a distressing impact on the quality of life and is challenging both for patients and physicians.Areas covered: This review focuses on the pathophysiology of constipation in IBS and presents current management options. It also covers the latest findings that may lead to novel pharmacological options in IBS-C management. The authors intend to highlight the results of published research including abstracts, records from the clinicaltrials.gov database (second and third phases of the study) and information from original FDA documents.Expert opinion: Current therapeutic options for IBS-C treatment are based on linaclotide, lubiprostone, plecanatide, and the reintroduced tegaserod. Drugs present on the market as well as those in pre-clinical development should increase the lower esophageal sphincter pressure, promote gastric motility, accelerate gastric emptying and improve gastro-duodenal coordination. Most significantly, they shall not induce severe side effects.
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Affiliation(s)
- Karolina Niewinna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Anna Zielińska
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Jakub Fichna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
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Avelar Rodriguez D, Ryan PM, Toro Monjaraz EM, Ramirez Mayans JA, Quigley EM. Small Intestinal Bacterial Overgrowth in Children: A State-Of-The-Art Review. Front Pediatr 2019; 7:363. [PMID: 31552207 PMCID: PMC6737284 DOI: 10.3389/fped.2019.00363] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/20/2019] [Indexed: 12/11/2022] Open
Abstract
Small intestinal bacterial overgrowth (SIBO) is a heterogenous and poorly understood entity characterised by an excessive growth of select microorganisms within the small intestine. This excessive bacterial biomass, in turn, disrupts host physiology in a myriad of ways, leading to gastrointestinal and non-gastrointestinal symptoms and complications. SIBO is a common cause of non-specific gastrointestinal symptoms in children, such as chronic abdominal pain, abdominal distention, diarrhoea, and flatulence, amongst others. In addition, it has recently been implicated in the pathophysiology of stunting, a disease that affects millions of children worldwide. Risk factors such as acid-suppressive therapies, alterations in gastrointestinal motility and anatomy, as well as impoverished conditions, have been shown to predispose children to SIBO. SIBO can be diagnosed via culture-dependant or culture-independent approaches. SIBO's epidemiology is limited due to the lack of uniformity and consensus of its diagnostic criteria, as well as the paucity of literature available. Antibiotics remain the first-line treatment option for SIBO, although emerging modalities such as probiotics and diet manipulation could also have a role. Herein, we present a state-of-the-art-review which aims to comprehensively outline the most current information on SIBO in children, with particular emphasis on the gut microbiota.
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Affiliation(s)
- David Avelar Rodriguez
- Pediatric Gastroenterology and Nutrition Unit, National Institute of Pediatrics, Mexico City, Mexico
| | | | | | | | - Eamonn Martin Quigley
- Lynda K. and David M. Underwood Center for Digestive Disorders, Houston Methodist Hospital, Houston, TX, United States
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Adike A, DiBaise JK. Small Intestinal Bacterial Overgrowth: Nutritional Implications, Diagnosis, and Management. Gastroenterol Clin North Am 2018; 47:193-208. [PMID: 29413012 DOI: 10.1016/j.gtc.2017.09.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small intestinal bacterial overgrowth (SIBO), characterized by the presence of excessive bacteria in the small intestine, is typically described as a malabsorptive syndrome occurring in the context of gut stasis syndromes. SIBO is now considered to be a disorder associated with diverse clinical conditions without classic risk factors for SIBO and a cause of several nonspecific gastrointestinal and nongastrointestinal symptoms. Because there is currently no gold standard for diagnosing SIBO, its prevalence and role in the pathogenesis of other diseases remain uncertain; as does optimal treatment of patients with relapsing symptoms.
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Affiliation(s)
- Abimbola Adike
- Division of Gastroenterology and Hepatology, Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA
| | - John K DiBaise
- Division of Gastroenterology and Hepatology, Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA.
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Stern EK, Brenner DM. Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. Clin Transl Gastroenterol 2018; 9:e134. [PMID: 29446765 PMCID: PMC5830546 DOI: 10.1038/ctg.2018.2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/11/2017] [Indexed: 11/15/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a common, heterogeneous disorder characterized by abdominal pain associated with changes in bowel habits. The pathogenesis of IBS is multifactorial and may relate to alterations in the gut microbiota, changes in visceral sensation and motility, and genetic and environmental factors. Administration of systemic antibiotics may increase the risk of IBS by altering gastrointestinal homeostasis. Therapeutic interventions for IBS with diarrhea that are thought to target alterations in the gut microbiota include the nonsystemic antibiotic rifaximin, the medical food serum-derived bovine immunoglobulin, prebiotics, probiotics, and dietary modification. SYN-010 is a modified-release statin formulation that reduces methane production by Methanobrevibacter smithii and is currently in development for the treatment of patients with constipation-predominant IBS. Use of these interventions in the management of patients with IBS may function to restore a healthy gut microbiota and ameliorate symptoms of IBS.
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Affiliation(s)
- Emily K Stern
- Division of Gastroenterology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Darren M Brenner
- Division of Gastroenterology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Hubert S, Chadwick A, Wacher V, Coughlin O, Kokai-Kun J, Bristol A. Development of a Modified-Release Formulation of Lovastatin Targeted to Intestinal Methanogens Implicated in Irritable Bowel Syndrome With Constipation. J Pharm Sci 2017; 107:662-671. [PMID: 28989013 DOI: 10.1016/j.xphs.2017.09.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/19/2022]
Abstract
There is growing evidence that methane production, predominantly by Methanobrevibacter smithii, in the intestines is a cause of constipation, pain, and bloating in irritable bowel syndrome with constipation (IBS-C). M smithii resides primarily in the large intestine but can also colonize the small intestine. In vitro studies found that the prodrug lactone form of lovastatin, found in cholesterol-lowering drugs, inhibited methane production in stool samples from patients with IBS-C. However, the cholesterol-lowering lovastatin β-hydroxyacid was ineffective at inhibiting methane production in this system. A considerable amount of lovastatin is converted to hydroxyacid in the stomach and is absorbed. It was hypothesized that galenic innovations could protect lovastatin from the stomach and allow release in 2 strategic locations, the duodenum and the ileocecal region, to reach M smithii. The desired release profile was achieved by developing an oral dosage form containing lovastatin and coated with 2 different enteric polymers that enabled a pH-dependent "dual pulse" drug release. Combinations of the 2 coated tablets were encapsulated together to deliver the desired amount of lovastatin to the targeted intestinal locations. The capsules have been tested in vitro and in vivo and show promise in treating IBS-C.
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Affiliation(s)
- Steven Hubert
- Synthetic Biologics, Inc., 9605 Medical Center Drive, Suite 270, Rockville, Maryland 20850.
| | - Alan Chadwick
- Aesica Formulation Development, Biocity, Pennyfoot Street, Nottingham NG1 1GF, UK
| | - Vince Wacher
- Synthetic Biologics, Inc., 9605 Medical Center Drive, Suite 270, Rockville, Maryland 20850
| | - Olivia Coughlin
- Synthetic Biologics, Inc., 9605 Medical Center Drive, Suite 270, Rockville, Maryland 20850
| | - John Kokai-Kun
- Synthetic Biologics, Inc., 9605 Medical Center Drive, Suite 270, Rockville, Maryland 20850
| | - Andrew Bristol
- Synthetic Biologics, Inc., 9605 Medical Center Drive, Suite 270, Rockville, Maryland 20850
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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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