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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [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: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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Shrestha S, Xue S, Raskin L. Competitive Reactions during Ethanol Chain Elongation Were Temporarily Suppressed by Increasing Hydrogen Partial Pressure through Methanogenesis Inhibition. Environ Sci Technol 2023; 57:3369-3379. [PMID: 36790331 PMCID: PMC9979639 DOI: 10.1021/acs.est.2c09014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 05/29/2023]
Abstract
Organic waste streams can be converted into high-value platform chemicals such as medium-chain carboxylic acids (MCCAs) using mixed microbial communities via chain elongation. However, the heterogeneity of waste streams and the use of complex microbial communities can lead to undesirable reactions, thus decreasing process efficiency. We explored suppressing excessive ethanol oxidation to acetate (EEO) by increasing the hydrogen partial pressure (PH2) through hydrogenotrophic methanogenesis inhibition by periodically adding 2-bromoethanesulfonate (2-BES) to an MCCA-producing bioreactor to reach 10 mM of 2-BES upon addition. The bioreactor was fed with pretreated food waste and brewery waste containing high concentrations of short-chain carboxylic acids and ethanol, respectively. While 2-BES addition initially reduced EEO, some methanogens (Methanobrevibacter spp.) persisted and resistant populations were selected over time. Besides changing the methanogenic community structure, adding 2-BES also changed the bacterial community structure due to its impact on PH2. While we demonstrated that PH2 could be manipulated using 2-BES to control EEO, methods that do not require the addition of a chemical inhibitor should be explored to maintain optimum PH2 for long-term suppression of EEO.
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Low A, Lee JKY, Gounot JS, Ravikrishnan A, Ding Y, Saw WY, Tan LWL, Moong DKN, Teo YY, Nagarajan N, Seedorf H. Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative. Microbiol Spectr 2022; 10:e0084922. [PMID: 35699469 PMCID: PMC9431525 DOI: 10.1128/spectrum.00849-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, Singapore
| | | | | | | | | | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik Ying Teo
- Genome Institute of Singapore, A*STAR, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
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Malik P, Trivedi S, Kolte A, Sejian V, Bhatta R, Rahman H. Diversity of rumen microbiota using metagenome sequencing and methane yield in Indian sheep fed on straw and concentrate diet. Saudi J Biol Sci 2022; 29:103345. [PMID: 35770269 PMCID: PMC9234715 DOI: 10.1016/j.sjbs.2022.103345] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteroidetes and Firmicutes were most prevalent bacteria in the sheep rumen. Bacteroidetes were negatively correlated with the Euryarchaeota. Archaea constituted ∼2.5% of the ruminal microbiota. Methanobrevibacter gottschalkii constituted > 50% of the ruminal archaea. Hydrogenotrophic methanogens distribution leads to the variability in methane yield.
An in vivo study aiming to investigate the rumen methanogens community structure was conducted in Mandya sheep fed on straw and concentrate diet. The ruminal fluid samples were collected and processed for unravelling the rumen microbiota and methanogens diversity. Further, the daily enteric methane emission and methane yield was also quantified using the SF6 tracer technique. Results indicated that the Bacteroidetes (∼57%) and Firmicutes (25%) were two prominent affiliates of the bacterial community. Archaea represented about 2.5% of the ruminal microbiota. Methanobacteriales affiliated methanogens were the most prevalent in sheep rumen. The study inveterate that the ruminal archaea community in sheep is composed of 9 genera and 18 species. Methanobrevibacter represented the largest genus of the archaeome, while methylotrophs genera constituted only 13% of the community. Methanobrevibacter gottschalkii was the prominent methanogen, and Methaobrevibacter ruminantium distributed at a lower frequency (∼2.5%). Among Methanomassiliicoccales, Group 12 sp. ISO4-H5 constituted the most considerable fraction (∼11%). KEGG reference pathway for methane metabolism indicated the formation of methane through hydrogenotrophic and methylotrophic pathways, whereas the acetoclastic pathway was not functional in sheep. The enteric methane emission and methane yield was 19.7 g/d and 20.8 g/kg DMI, respectively. Various species of Methanobrevibacter were differently correlated, and the distribution of hydrogenotrophic methanogens mainly explained the variability in methane yield between the individual sheep. It can be inferred from the study that the hydrogenotrophic methanogens dominate the rumen archaeal community in sheep and methylotrophic/aceticlastic methanogens represent a minor fraction of the community. Further studies are warranted for establishing the metabolic association between the prevalent hydrogenotrophs and methylotrophs to identify the key reaction for reducing methane emission.
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Affiliation(s)
- P.K. Malik
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
- Corresponding author.
| | - S. Trivedi
- Bioenergetics and Environmental Science Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - A.P. Kolte
- Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - V. Sejian
- Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - R. Bhatta
- Director, ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India
| | - H. Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110 012, India
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Catlett JL, Carr S, Cashman M, Smith MD, Walter M, Sakkaff Z, Kelley C, Pierobon M, Cohen MB, Buan NR. Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter. Microbiol Spectr 2022; 10:e0106722. [PMID: 35536023 PMCID: PMC9241691 DOI: 10.1128/spectrum.01067-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022] Open
Abstract
Trophic interactions between microbes are postulated to determine whether a host microbiome is healthy or causes predisposition to disease. Two abundant taxa, the Gram-negative heterotrophic bacterium Bacteroides thetaiotaomicron and the methanogenic archaeon Methanobrevibacter smithii, are proposed to have a synergistic metabolic relationship. Both organisms play vital roles in human gut health; B. thetaiotaomicron assists the host by fermenting dietary polysaccharides, whereas M. smithii consumes end-stage fermentation products and is hypothesized to relieve feedback inhibition of upstream microbes such as B. thetaiotaomicron. To study their metabolic interactions, we defined and optimized a coculture system and used software testing techniques to analyze growth under a range of conditions representing the nutrient environment of the host. We verify that B. thetaiotaomicron fermentation products are sufficient for M. smithii growth and that accumulation of fermentation products alters secretion of metabolites by B. thetaiotaomicron to benefit M. smithii. Studies suggest that B. thetaiotaomicron metabolic efficiency is greater in the absence of fermentation products or in the presence of M. smithii. Under certain conditions, B. thetaiotaomicron and M. smithii form interspecies granules consistent with behavior observed for syntrophic partnerships between microbes in soil or sediment enrichments and anaerobic digesters. Furthermore, when vitamin B12, hematin, and hydrogen gas are abundant, coculture growth is greater than the sum of growth observed for monocultures, suggesting that both organisms benefit from a synergistic mutual metabolic relationship. IMPORTANCE The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions. We studied the interactions between two dominant human gut microbes, B. thetaiotaomicron and M. smithii, using a seven-component culturing approach that allows the systematic examination of the metabolic complexity of this binary microbial system. By combining high-throughput methods with machine learning techniques, we were able to investigate the interactions between two dominant genera of the gut microbiome in a wide variety of environmental conditions. Our approach can be broadly applied to studying microbial interactions and may be extended to evaluate and curate computational metabolic models. The software tools developed for this study are available as user-friendly tutorials in the Department of Energy KBase.
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Affiliation(s)
- Jennie L. Catlett
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sean Carr
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mikaela Cashman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Megan D. Smith
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mary Walter
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zahmeeth Sakkaff
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Christine Kelley
- Department of Mathematics, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Massimiliano Pierobon
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Myra B. Cohen
- Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
| | - Nicole R. Buan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Teigen L, Mathai PP, Matson M, Lopez S, Kozysa D, Kabage AJ, Hamilton MJ, Vaughn BP, Sadowsky MJ, Khoruts A. Methanogen Abundance Thresholds Capable of Differentiating In Vitro Methane Production in Human Stool Samples. Dig Dis Sci 2021; 66:3822-30. [PMID: 33247793 DOI: 10.1007/s10620-020-06721-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/15/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Intestinal methane (CH4) gas production has been associated with a number of clinical conditions and may have important metabolic and physiological effects. AIMS In this study, taxonomic and functional gene analyses and in vitro CH4 gas measurements were used to determine if molecular markers can potentially serve as clinical tests for colonic CH4 production. METHODS We performed a cross-sectional study involving full stool samples collected from 33 healthy individuals. In vitro CH4 gas measurements were obtained after 2-h incubation of stool samples and used to characterize samples as CH4 positive (CH4+) and CH4 negative (CH4-; n = 10 and 23, respectively). Next, we characterized the fecal microbiota through high-throughput DNA sequencing with a particular emphasis on archaeal phylum Euryarchaeota. Finally, qPCR analyses, targeting the mcrA gene, were done to determine the ability to differentiate CH4+ versus CH4- samples and to delineate major methanogen species associated with CH4 production. RESULTS Methanobrevibacter was found to be the most abundant methane producer and its relative abundance provides a clear distinction between CH4+ versus CH4- samples. Its sequencing-based relative abundance detection threshold for CH4 production was calculated to be 0.097%. The qPCR-based detection threshold separating CH4+ versus CH4- samples, based on mcrA gene copies, was 5.2 × 105 copies/g. CONCLUSION Given the decreased time-burden placed on patients, a qPCR-based test on a fecal sample can become a valuable tool in clinical assessment of CH4 producing status.
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. Microbiome 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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Kumpitsch C, Fischmeister FPS, Mahnert A, Lackner S, Wilding M, Sturm C, Springer A, Madl T, Holasek S, Högenauer C, Berg IA, Schoepf V, Moissl-Eichinger C. Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans. Microbiome 2021; 9:193. [PMID: 34560884 PMCID: PMC8464155 DOI: 10.1186/s40168-021-01130-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood. RESULTS We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH4 breath content 5-75 ppm) and low emitters (CH4 < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis. CONCLUSIONS This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.
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Affiliation(s)
- Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Florian Ph. S. Fischmeister
- Department of Psychology, University of Graz, 8010 Graz, Austria
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sonja Lackner
- Division of Immunology and Pathophysiology, Medical University of Graz, 8010 Graz, Austria
| | - Marilena Wilding
- Department of Psychology, University of Graz, 8010 Graz, Austria
| | - Corina Sturm
- Department of Psychology, University of Graz, 8010 Graz, Austria
| | - Anna Springer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, 8010 Graz, Austria
- BioTechMed, 8010 Graz, Austria
| | - Sandra Holasek
- Division of Immunology and Pathophysiology, Medical University of Graz, 8010 Graz, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Ivan A. Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Veronika Schoepf
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed, 8010 Graz, Austria
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Dykstra CM, Pavlostathis SG. Hydrogen sulfide affects the performance of a methanogenic bioelectrochemical system used for biogas upgrading. Water Res 2021; 200:117268. [PMID: 34098269 DOI: 10.1016/j.watres.2021.117268] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Methanogenic bioelectrochemical systems (BESs) can convert carbon dioxide (CO2) to methane (CH4) and may be used for anaerobic digester biogas upgrading. However, the effect of hydrogen sulfide (H2S), a common biogas component, on BES performance is unknown. Thus, the objective of this study was to assess the effect of H2S addition to the cathode headspace on BES performance at a range of initial gas-phase H2S concentrations (0-6% v/v), as well as its effect on the anode and cathode microbial communities. As the initial cathode headspace H2S increased from 0 to 2% (v/v), biocathodic CH4 production increased by two-fold to 3.56 ± 0.36 mmol/L-d, due to dissolved H2S transport from the cathode to the anode where H2S was oxidized. Elemental sulfur and sulfate were H2S oxidation products detected in the anode. Above 3% initial cathode headspace H2S, biocathodic CH4 production declined due to inhibition. A phylotype most closely related to Methanobrevibacter arboriphilus dominated the cathode archaeal communities. In the sulfide-amended BES, a phylotype similar to the exoelectrogen Ochrobactrum anthropi was enriched in both the anode and cathode, whereas phylotypes related to sulfate-reducing and sulfur oxidizing Bacteria were detected in the bioanode. Thus, sulfide transport and oxidation in the anode play an important role in methanogenic BESs treating sulfide-bearing biogas.
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Affiliation(s)
- Christy M Dykstra
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512, United States; Department of Civil, Construction and Environmental Engineering, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, United States.
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512, United States
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Horváthová T, Šustr V, Chroňáková A, Semanová S, Lang K, Dietrich C, Hubáček T, Ardestani MM, Lara AC, Brune A, Šimek M. Methanogenesis in the Digestive Tracts of the Tropical Millipedes Archispirostreptus gigas (Diplopoda, Spirostreptidae) and Epibolus pulchripes (Diplopoda, Pachybolidae). Appl Environ Microbiol 2021; 87:e0061421. [PMID: 34020937 DOI: 10.1128/AEM.00614-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanogens represent the final decomposition step in anaerobic degradation of organic matter, occurring in the digestive tracts of various invertebrates. However, factors determining their community structure and activity in distinct gut sections are still debated. In this study, we focused on the tropical millipede species Archispirostreptus gigas (Diplopoda, Spirostreptidae) and Epibolus pulchripes (Diplopoda, Pachybolidae), which release considerable amounts of methane. We aimed to characterize relationships between physicochemical parameters, methane production rates, and methanogen community structure in the two major gut sections, midgut and hindgut. Microsensor measurements revealed that both sections were strictly anoxic, with reducing conditions prevailing in both millipedes. Hydrogen concentration peaked in the anterior hindgut of E. pulchripes. In both species, the intestinal pH was significantly higher in the hindgut than in the midgut. An accumulation of acetate and formate in the gut indicated bacterial fermentation activities in the digestive tracts of both species. Phylogenetic analysis of 16S rRNA genes showed a prevalence of Methanobrevibacter spp. (Methanobacteriales), accompanied by a small fraction of so-far-unclassified "Methanomethylophilaceae" (Methanomassiliicoccales), in both species, which suggests that methanogenesis is mostly hydrogenotrophic. We conclude that anoxic conditions, negative redox potential, and bacterial production of hydrogen and formate promote gut colonization by methanogens. The higher activities of methanogens in the hindgut are explained by the higher pH of this compartment and their association with ciliates, which are restricted to this compartment and present an additional source of methanogenic substrates. IMPORTANCE Methane (CH4) is the second most important atmospheric greenhouse gas after CO2 and is believed to account for 17% of global warming. Methanogens are a diverse group of archaea and can be found in various anoxic habitats, including digestive tracts of plant-feeding animals. Termites, cockroaches, the larvae of scarab beetles, and millipedes are the only arthropods known to host methanogens and emit large amounts of methane. Millipedes are ranked as the third most important detritivores after termites and earthworms, and they are considered keystone species in many terrestrial ecosystems. Both methane-producing and non-methane-emitting species of millipedes have been observed, but what limits their methanogenic potential is not known. In the present study, we show that physicochemical gut conditions and the distribution of symbiotic ciliates are important factors determining CH4 emission in millipedes. We also found close similarities to other methane-emitting arthropods, which might be associated with their similar plant-feeding habits.
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Kuznetsova V, Tyakht A, Akhmadishina L, Odintsova V, Klimenko N, Kostryukova E, Vakhitova M, Grigoryeva T, Malanin S, Vladimirtsev V, Nikitina R, Volok V, Osakovskiy V, Sivtseva T, Platonov F, Alexeev D, Karganova G. Gut microbiome signature of Viliuisk encephalomyelitis in Yakuts includes an increase in microbes linked to lean body mass and eating behaviour. Orphanet J Rare Dis 2020; 15:327. [PMID: 33218345 PMCID: PMC7678198 DOI: 10.1186/s13023-020-01612-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Viliuisk encephalomyelitis (VE) is a rare endemic neurodegenerative disease occurring in the Yakut population of Northeastern Siberia. The main clinical features of VE are spasticity, dysarthria, dementia, central paresis and paralysis, and cortical atrophy observed via MRI. Many hypotheses have been proposed regarding its etiology, including infectious agents, genetics, environmental factors, and immunopathology. Each of these hypotheses has been supported to some extent by epidemiological and experimental data. Nevertheless, none of them has been decisively proven. Gut microbiome is one of the factors that might be involved in VE pathogenesis. RESULTS Here we performed a pilot survey of the stool microbiomes of Yakut subjects with VE (n = 6) and without VE (n = 11). 16S rRNA sequencing showed that in comparison with the control group, the Yakuts with VE had increased proportions of Methanobrevibacter and Christensenella, which are reported to be linked to body mass index, metabolism, dietary habits and potentially to neurodegenerative disorders. The identified associations suggest that the microbiome may be involved in VE. Overall, the Yakut microbiome was quite specific in comparison with other populations, such as metropolitan Russians and native inhabitants of the Canadian Arctic. CONCLUSIONS Describing the gut microbiome of indigenous human populations will help to elucidate the impact of dietary and environmental factors on microbial community structure and identify risks linked to the lifestyles of such groups as well as endemic diseases.
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Affiliation(s)
- Veronika Kuznetsova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology of Russian Academy of Science, Vavilova Str. 34/5, 119334, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Kerchenskaya Str. 1A, Moscow, Russian Federation, 117303
| | - Alexander Tyakht
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology of Russian Academy of Science, Vavilova Str. 34/5, 119334, Moscow, Russian Federation.
- Atlas Biomed Group - Knomics LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK.
| | - Lyudmila Akhmadishina
- Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991, Moscow, Russian Federation
| | - Vera Odintsova
- Atlas Biomed Group - Knomics LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology of Russian Academy of Science, Vavilova Str. 34/5, 119334, Moscow, Russian Federation
- Atlas Biomed Group - Knomics LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK
| | - Elena Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, 119435, Moscow, Russian Federation
| | - Maria Vakhitova
- Moscow Institute of Physics and Technology, Kerchenskaya Str. 1A, Moscow, Russian Federation, 117303
- Federal Research and Clinical Centre of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1a, 119435, Moscow, Russian Federation
| | - Tatyana Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, K. Marx Str. 18, 420012, Kazan, Russian Federation
| | - Sergey Malanin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, K. Marx Str. 18, 420012, Kazan, Russian Federation
| | - Vsevolod Vladimirtsev
- Research Center of Medical Institute, M.K. Ammosov North-Eastern Federal University, Belinsky Str. 58, 677027, Yakutsk, Russian Federation
| | - Raisa Nikitina
- Research Center of Medical Institute, M.K. Ammosov North-Eastern Federal University, Belinsky Str. 58, 677027, Yakutsk, Russian Federation
| | - Viktor Volok
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI "Chumakov FSC R&D IBP RAS), prem. 8, k.17, pos. Institut Poliomyelita, poselenie Moskovskiy, 108819, Moscow, Russian Federation
| | - Vladimir Osakovskiy
- Research Center of Medical Institute, M.K. Ammosov North-Eastern Federal University, Belinsky Str. 58, 677027, Yakutsk, Russian Federation
| | - Tatiana Sivtseva
- Research Center of Medical Institute, M.K. Ammosov North-Eastern Federal University, Belinsky Str. 58, 677027, Yakutsk, Russian Federation
| | - Fyodor Platonov
- Research Center of Medical Institute, M.K. Ammosov North-Eastern Federal University, Belinsky Str. 58, 677027, Yakutsk, Russian Federation
| | - Dmitry Alexeev
- Atlas Biomed Group - Knomics LLC, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK
- ITMO University, Kronverkskiy pr. 49, 197101, Saint-Petersburg, Russian Federation
| | - Galina Karganova
- Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991, Moscow, Russian Federation
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI "Chumakov FSC R&D IBP RAS), prem. 8, k.17, pos. Institut Poliomyelita, poselenie Moskovskiy, 108819, Moscow, Russian Federation
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Drancourt M, Djemai K, Gouriet F, Grine G, Loukil A, Bedotto M, Levasseur A, Lepidi H, Bou-Khalil J, Khelaifia S, Raoult D. Methanobrevibacter smithii archaemia in febrile patients with bacteremia, including those with endocarditis. Clin Infect Dis 2020; 73:e2571-e2579. [PMID: 32668457 DOI: 10.1093/cid/ciaa998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 01/21/2020] [Accepted: 07/10/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The spectrum of infections caused by the emerging opportunistic pathogens methanogens which escape routine detection remains to be described. To determine the prevalence of archaemia, we searched for methanogens in the blood of febrile patients using specific tools. METHODS We conducted a prospective study at Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France, September 2018 - April 2020, enrolling 7,716 blood culture samples routinely collected in patients with fever. Blood samples were screened by specific PCR assays for the presence of methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations. RESULTS PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles that contained cultures collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, fermentative Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five blood samples, and M. smithii was isolated via culture in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data.Three patients, all diagnosed with infectious mitral endocarditis, were diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues. CONCLUSIONS Using appropriate methods of detection, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.
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Affiliation(s)
- Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Kenza Djemai
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Marielle Bedotto
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | | | | | - Didier Raoult
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Xiang Z, Tong W, Guo Z, Xu Y, Guo J, Ruan Y, Zhao P. Rat H1 parvovirus infection leads to alterations in gut microbiota. Pathog Dis 2020; 77:5585884. [PMID: 31603501 DOI: 10.1093/femspd/ftz058] [Citation(s) in RCA: 2] [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: 05/20/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023] Open
Abstract
H1 parvovirus (H1PV) infection in rats is of concern to the research community as infection may compromise rodent-based experiments. The aim of this study was to evaluate the influence of H1PV infection on rat gut microbiota. Inbred Wistar rats were infected with H1PV by routine gavage and clinical signs were recorded. Gross anatomical and histopathological examination of the gut was performed, as was immune cytokine analysis. The cecal contents were also collected for 16S rRNA sequencing. Gross anatomical examination showed distention of the ileum associated with flatulence after infection, while histopathological examination showed hyperemia and inflammatory cell infiltration in the ileum. Upregulation of the interleukin-6 in sera in H1PV infected rats was also detected. The gut microbiota had been significantly changed in H1PV infected rats: there was a reduction in several bacteria species including probiotic bacteria from the genera Parabacteroides and Butyricicoccus, while others were increased, including those from the genera Methanobrevibacter and Syntrophococcus. Taken together, these results demonstrate that chronic H1PV infection in rats leads to gastrointestinal inflammation with flatulence. The gut microbiota alterations were associated with decreased polymorphisms, reduced abundance of probiotic bacteria and increased abundance of methane-producing bacteria.
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Affiliation(s)
- Zhiguang Xiang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Wei Tong
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Zhi Guo
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Yanfeng Xu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Jianguo Guo
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Yanshuo Ruan
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
| | - Peng Zhao
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Panjiayuan nanli #5, Chaoyang District, Beijing 100021, China
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14
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Andrade BGN, Bressani FA, Cuadrat RRC, Tizioto PC, de Oliveira PSN, Mourão GB, Coutinho LL, Reecy JM, Koltes JE, Walsh P, Berndt A, Palhares JCP, Regitano LCA. The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen. J Anim Sci Biotechnol 2020; 11:6. [PMID: 32123563 PMCID: PMC7038601 DOI: 10.1186/s40104-019-0422-x] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022] Open
Abstract
Background The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa. Results We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population. Conclusions Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.
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Affiliation(s)
| | | | - Rafael R C Cuadrat
- 2Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | | | | | - Gerson B Mourão
- 4Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz L Coutinho
- 4Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - James M Reecy
- 5Department of Animal Science, Iowa State University, Ames, IA USA
| | - James E Koltes
- 5Department of Animal Science, Iowa State University, Ames, IA USA
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15
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Renelies-Hamilton J, Noguera-Julian M, Parera M, Paredes R, Pacheco L, Dacal E, Saugar JM, Rubio JM, Poulsen M, Köster PC, Carmena D. Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal. Infect Genet Evol 2019; 74:104010. [PMID: 31442596 DOI: 10.1016/j.meegid.2019.104010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/02/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Gut parasites exert an important influence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic inflammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species. AIMS We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans. METHODS Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis, Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for differences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples. RESULTS For Blastocystis, twelve differentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus-Methanobrevibacter enterotype markers, replicate findings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis, unlike Strongyloides, is associated to a "poor health" gut microbiome, as does the fact that Faecalibacterium, a bacterium with gut protective traits, is absent in Blastocystis-positive samples. Strongyloides was associated to Alloprevotella and five other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite-specific niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disentangle biological from artefactual associations between gut microbiomes and parasites.
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Affiliation(s)
- Justinn Renelies-Hamilton
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Liliana Pacheco
- Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal
| | - Elena Dacal
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Saugar
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Rubio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
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Carbone V, Schofield LR, Sang C, Sutherland-Smith AJ, Ronimus RS. Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid. Proteins 2018; 86:1306-1312. [PMID: 30242905 DOI: 10.1002/prot.25606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/01/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
Abstract
The crystal structure of UDP-N-acetylglucosamine 4-epimerase (UDP-GlcNAc 4-epimerase; WbpP; EC 5.1.3.7), from the archaeal methanogen Methanobrevibacter ruminantium strain M1, was determined to a resolution of 1.65 Å. The structure, with a single monomer in the crystallographic asymmetric unit, contained a conserved N-terminal Rossmann-fold for nucleotide binding and an active site positioned in the C-terminus. UDP-GlcNAc 4-epimerase is a member of the short-chain dehydrogenases/reductases superfamily, sharing sequence motifs and structural elements characteristic of this family of oxidoreductases and bacterial 4-epimerases. The protein was co-crystallized with coenzyme NADH and UDP-N-acetylmuramic acid, the latter an unintended inclusion and well known product of the bacterial enzyme MurB and a critical intermediate for bacterial cell wall synthesis. This is a non-native UDP sugar amongst archaea and was most likely incorporated from the E. coli expression host during purification of the recombinant enzyme.
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Affiliation(s)
- Vincenzo Carbone
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Linley R Schofield
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carrie Sang
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Ron S Ronimus
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Weimar MR, Cheung J, Dey D, McSweeney C, Morrison M, Kobayashi Y, Whitman WB, Carbone V, Schofield LR, Ronimus RS, Cook GM. Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions. Appl Environ Microbiol 2017; 83:e00396-17. [PMID: 28526787 DOI: 10.1128/AEM.00396-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H2 and CO2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions.IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions.
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Danielsson R, Dicksved J, Sun L, Gonda H, Müller B, Schnürer A, Bertilsson J. Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure. Front Microbiol 2017; 8:226. [PMID: 28261182 PMCID: PMC5313486 DOI: 10.3389/fmicb.2017.00226] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [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: 09/07/2016] [Accepted: 01/31/2017] [Indexed: 11/13/2022] Open
Abstract
Methane (CH4) is produced as an end product from feed fermentation in the rumen. Yield of CH4 varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH4 emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH4 emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH4 emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters (P < 0.01) that were related to CH4 production. One cluster was associated with low CH4 production (referred to as cluster L) whereas the other cluster was associated with high CH4 production (cluster H) and the medium emitters occurred in both clusters. The differences between clusters were primarily linked to differential abundances of certain OTUs belonging to Prevotella. Moreover, several OTUs belonging to the family Succinivibrionaceae were dominant in samples belonging to cluster L. Fermentation pattern of volatile fatty acids showed that proportion of propionate was higher in cluster L, while proportion of butyrate was higher in cluster H. No difference was found in milk production or organic matter digestibility between cows. Cows in cluster L had lower CH4/kg energy corrected milk (ECM) compared to cows in cluster H, 8.3 compared to 9.7 g CH4/kg ECM, showing that low CH4 cows utilized the feed more efficient for milk production which might indicate a more efficient microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations.
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Affiliation(s)
- Rebecca Danielsson
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Li Sun
- Department of Microbiology, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Horacio Gonda
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNCPBA Tandil, Argentina
| | - Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Jan Bertilsson
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences Uppsala, Sweden
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Bharathi M, Chellapandi P. Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea. Mol Phylogenet Evol 2016; 107:293-304. [PMID: 27864137 DOI: 10.1016/j.ympev.2016.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 03/30/2016] [Revised: 09/17/2016] [Accepted: 11/13/2016] [Indexed: 02/01/2023]
Abstract
Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter. Comparison of the phylogenetic and metabolic markers was suggested for its archaeal metabolic core lineage that might have evolved from Methanothermobacter. Orthologous genes involved in its hydrogenotrophic methanogenesis might be acquired from intergenomic ancestry of Methanothermobacter via Methanobacterium formicicum. Formate dehydrogenase (fdhAB) coding gene cluster and carbon monoxide dehydrogenase (cooF) coding gene might have evolved from duplication events within Methanobrevibacter-Methanothermobacter lineage, and fdhCD gene cluster acquired from bacterial origins. Genome-wide metabolic survey found the existence of four novel pathways viz. l-tyrosine catabolism, mevalonate pathway II, acyl-carrier protein metabolism II and glutathione redox reactions II in MRU. Finding of these pathways suggested that MRU has shown a metabolic potential to tolerate molecular oxygen, antimicrobial metabolite biosynthesis and atypical lipid composition in cell wall, which was acquainted by metabolic cross-talk with mammalian bacterial origins. We conclude that coevolution of genomic contents between Methanobrevibacter and Methanothermobacter provides a clue to understand the metabolic adaptation of MRU in the rumen at different environmental niches.
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Affiliation(s)
- M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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Cao Z, Liang JB, Liao XD, Wright AD, Wu YB, Yu B. Effect of dietary fiber on the methanogen community in the hindgut of Lantang gilts. Animal 2016; 10:1666-76. [PMID: 27052363 DOI: 10.1017/S1751731116000525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The primary objective of this study was to investigate the effect of dietary fiber on methanogenic diversity and community composition in the hindgut of indigenous Chinese Lantang gilts to explain the unexpected findings reported earlier that Lantang gilts fed low-fiber diet (LFD) produced more methane than those fed high-fiber diet (HFD). In total, 12 Lantang gilts (58.7±0.37 kg) were randomly divided into two dietary groups (six replicates (pigs) per group) and fed either LFD (NDF=201.46 g/kg) or HFD (NDF=329.70 g/kg). Wheat bran was the main source of fiber for the LFD, whereas ground rice hull (mixture of rice hull and rice bran) was used for the HFD. Results showed that the methanogens in the hindgut of Lantang gilts belonged to four known species (Methanobrevibacter ruminantium, Methanobrevibacter wolinii, Methanosphaera stadtmanae and Methanobrevibacter smithii), with about 89% of the methanogens belonging to the genus Methanobrevibacter. The 16S ribosomal RNA (rRNA) gene copies of Methanobrevibacter were more than three times higher (P0.05) was observed in 16S rRNA gene copies of Fibrobacter succinogenes between the two dietary groups, and 18S rRNA gene copies of anaerobic fungi in gilts fed LFD were lower than (P<0.05) those fed HFD. To better explain the effect of different fiber source on the methanogen community, a follow-up in vitro fermentation using a factorial design comprised of two inocula (prepared from hindgut content of gilts fed two diets differing in their dietary fiber)×four substrates (LFD, HFD, wheat bran, ground rice hull) was conducted. Results of the in vitro fermentation confirmed that the predominant methanogens belonged to the genus of Methanobrevibacter, and about 23% methanogens was found to be distantly related (90%) to Thermogymnomonas acidicola. In vitro fermentation also seems to suggest that fiber source did change the methanogens community. Although the density of Methanobrevibacter species was positively correlated with CH4 production in both in vivo (P<0.01, r=0.737) and in vitro trials (P<0.05, r=0.854), which could partly explain the higher methane production from gilts fed LFD compared with those in the HFD group. Further investigation is needed to explain how the rice hull affected the methanogens and inhibited CH4 emission from gilts fed HFD.
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Siegert M, Li XF, Yates MD, Logan BE. The presence of hydrogenotrophic methanogens in the inoculum improves methane gas production in microbial electrolysis cells. Front Microbiol 2015; 5:778. [PMID: 25642216 PMCID: PMC4295556 DOI: 10.3389/fmicb.2014.00778] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 09/05/2014] [Accepted: 12/18/2014] [Indexed: 11/26/2022] Open
Abstract
High current densities in microbial electrolysis cells (MECs) result from the predominance of various Geobacter species on the anode, but it is not known if archaeal communities similarly converge to one specific genus. MECs were examined here on the basis of maximum methane production and current density relative to the inoculum community structure. We used anaerobic digester (AD) sludge dominated by acetoclastic Methanosaeta, and an anaerobic bog sediment where hydrogenotrophic methanogens were detected. Inoculation using solids to medium ratio of 25% (w/v) resulted in the highest methane production rates (0.27 mL mL−1 cm−2, gas volume normalized by liquid volume and cathode projected area) and highest peak current densities (0.5 mA cm−2) for the bog sample. Methane production was independent of solid to medium ratio when AD sludge was used as the inoculum. 16S rRNA gene community analysis using pyrosequencing and quantitative PCR confirmed the convergence of Archaea to Methanobacterium and Methanobrevibacter, and of Bacteria to Geobacter, despite their absence in AD sludge. Combined with other studies, these findings suggest that Archaea of the hydrogenotrophic genera Methanobacterium and Methanobrevibacter are the most important microorganisms for methane production in MECs and that their presence in the inoculum improves the performance.
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Affiliation(s)
- Michael Siegert
- Department of Civil and Environmental Engineering, Penn State University University Park, PA, USA
| | - Xiu-Fen Li
- School of Environmental and Civil Engineering, Jiangnan University Wuxi, China
| | - Matthew D Yates
- Department of Civil and Environmental Engineering, Penn State University University Park, PA, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, Penn State University University Park, PA, USA
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Aghasadeghi MR, Delbaz SA, Sadat SM, Siadat SD, Ardestani MS, Rahimi P, Bolhassani A, Roudsari RV, Bahramali G, Motevalli F, Davari M, Vakily H, Salmani AS, Nobari MB. Induction of Strong and Specific Humoral and T-helper 1 Cellular Responses by HBsAg Entrapped in the Methanobrevibacter smithii Archaeosomes. Avicenna J Med Biotechnol 2014; 6:238-45. [PMID: 25414786 PMCID: PMC4224663] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/12/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Application of adjuvants with microbial origins is a recently highlighted approach in the vaccinology trials. Archaeosomes are among these microbial compounds with both adjuvant and liposomal activities and features. METHODS In the present study, recombinant HBsAg encapsulated into Methanobrevibacter smithii (M. smithii) archaeosomes. Balb/c mice immunized with this compound and humoral and cytokine secretion pattern of immunized models analyzed. RESULTS Frequency of IFN-γ secreting cells in the HBsAg-containing archaeosomes group was significantly higher than HBsAg and HBsAg(+)C/IFA groups (p≤0.05). IgG2a titer in the sera of HBsAg-containing archaeosomes group was also significantly higher than this subclass titer in the other groups (p≤ 0.05). CONCLUSION Analysis of induced responses revealed the immunopotentiating characteristics of M. smithii archaeosomes in the induction of T-helper 1 responses according to the dominance of IgG2a subtype and IFN-γ secreting splenocytes of immunized mice.
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Affiliation(s)
| | - Seyed Ali Delbaz
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Pooneh Rahimi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Golnaz Bahramali
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Fateme Motevalli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Davari
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Habib Vakily
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Sharifat Salmani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran,Corresponding author: Ali Sharifat Salmani, Ph.D., Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran. Tel: +98 21 66953311. E-mail:
| | - Maryam Borhan Nobari
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Ali Sharifat Salmani, Ph.D., Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran. Tel: +98 21 66953311. E-mail:
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Abstract
Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B′ and B′′ subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.
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Affiliation(s)
- S C Leahy
- New Zealand Agricultural Greenhouse Gas Research Centre ; Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, New Zealand
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