scholarly journals Energetics and Application of Heterotrophy in Acetogenic Bacteria

2016 ◽  
Vol 82 (14) ◽  
pp. 4056-4069 ◽  
Author(s):  
Kai Schuchmann ◽  
Volker Müller
Keyword(s):  
Anaerobic Bacteria ◽  
Metabolic Flexibility ◽  
Strictly Anaerobic ◽  
Autotrophic Growth ◽  
Content Type ◽  
Anoxic Environments ◽  
Acetogenic Bacteria ◽  
Heterotrophic Metabolism ◽  
Global Carbon ◽  
Substrate Spectrum

ABSTRACTAcetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogenAcetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens.

scholarly journals Alanine, a Novel Growth Substrate for the Acetogenic BacteriumAcetobacterium woodii

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Judith Dönig ◽  
Volker Müller
Keyword(s):  
Amino Acids ◽  
Ph Regulation ◽  
Anaerobic Bacteria ◽  
Strictly Anaerobic ◽  
Growth Substrate ◽  
Acetobacterium Woodii ◽  
Content Type ◽  
Important Group ◽  
Acetogenic Bacteria ◽  
A Minor

ABSTRACTAcetogenic bacteria are an ecophysiologically important group of strictly anaerobic bacteria that grow lithotrophically on H2plus CO2or on CO or heterotrophically on different substrates such as sugars, alcohols, aldehydes, or acids. Amino acids are rarely used. Here, we describe that the model acetogenAcetobacterium woodiican use alanine as the sole carbon and energy source, which is in contrast to the description of the type strain. The alanine degradation genes have been identified and characterized. A key to alanine degradation is an alanine dehydrogenase which has been characterized biochemically. The resulting pyruvate is further degraded to acetate by the known pathways involving the Wood-Ljungdahl pathway. Our studies culminate in a metabolic and bioenergetic scheme for alanine-dependent acetogenesis inA. woodii.IMPORTANCEPeptides and amino acids are widespread in nature, but there are only a few reports that demonstrated use of amino acids as carbon and energy sources by acetogenic bacteria, a central and important group in the anaerobic food web. Our finding thatA. woodiican perform alanine oxidation coupled to reduction of carbon dioxide not only increases the number of substrates that can be used by this model acetogen but also raises the possibility that other acetogens may also be able to use alanine. Indeed, the alanine genes are also present in at least two more acetogens, for which growth on alanine has not been reported so far. Alanine may be a promising substrate for industrial fermentations, since acid formation goes along with the production of a base (NH3) and pH regulation is a minor issue.

scholarly journals How the Anaerobic Enteropathogen Clostridioides difficile Tolerates Low O2 Tensions

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Nicolas Kint ◽  
Carolina Alves Feliciano ◽  
Maria C. Martins ◽  
Claire Morvan ◽  
Susana F. Fernandes ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Anaerobic Bacteria ◽  
Growth Defect ◽  
Strictly Anaerobic ◽  
Low Oxygen ◽  
Air Exposure ◽  
Vegetative Cells ◽  
Content Type ◽  
Clostridioides Difficile

ABSTRACT Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon. IMPORTANCE Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract.

scholarly journals Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Elizabeth A. McDaniel ◽  
Benjamin D. Peterson ◽  
Sarah L. R. Stevens ◽  
Patricia Q. Tran ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
Carbon Fixation ◽  
Anaerobic Bacteria ◽  
Inorganic Mercury ◽  
Metal Resistance ◽  
Metabolic Flexibility ◽  
Metabolic Diversity ◽  
Content Type ◽  
Methylmercury Production

ABSTRACT Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment. IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

scholarly journals Mercury Methylation and Demethylation in Anoxic Lake Sediments and by Strictly Anaerobic Bacteria

1998 ◽  
Vol 64 (3) ◽  
pp. 1013-1017 ◽  
Author(s):  
K.-R. Pak ◽  
R. Bartha
Keyword(s):  
Organic Matter ◽  
Anaerobic Bacteria ◽  
Mercury Methylation ◽  
Strictly Anaerobic ◽  
Anoxic Sediment ◽  
Acetogenic Bacteria ◽  
High Potentials ◽  
High Mercury ◽  
Pure Cultures ◽  
Sediment Ph

ABSTRACT After spiking anoxic sediment slurries of three acidic oligotrophic lakes with either HgCl2 at 1.0 μg/ml or CH3HgI at 0.1 μg/ml, both mercury methylation and demethylation rates were measured. High mercury methylation potentials were accompanied by high demethylation potentials in the same sediment. These high potentials correlated positively with the concentrations of organic matter and dissolved sulfate in the sediment and with mercury levels in fish. Adjustment of the acidic sediment pH to neutrality failed to influence either the methylation or the demethylation rate of mercury. The opposing methylation and demethylation processes converged to establish similar Hg2+-CH3Hg+equilibria in all three sediments. Because of their metabolic dominance in anoxic sediments, mercury methylation and demethylation in pure cultures of sulfidogenic, methanogenic, and acetogenic bacteria were also measured. Sulfidogens both methylated and demethylated mercury, but the methanogen tested only catalyzed demethylation and the acetogen neither methylated nor demethylated mercury.

scholarly journals Brockarchaeota, a novel archaeal lineage capable of methylotrophy

2020 ◽  
Author(s):  
Valerie De Anda ◽  
Lin-Xing Chen ◽  
Nina Dombrowski ◽  
Zhengshuang Hua ◽  
Hong-Chen Jiang ◽  
...  
Keyword(s):  
Hot Springs ◽  
Phylogenetic Analyses ◽  
Methanogenic Archaea ◽  
Sulfate Reducing ◽  
Anoxic Environments ◽  
Archaeal Lineage ◽  
Acetogenic Bacteria ◽  
Reducing Bacteria ◽  
Globally Distributed ◽  
Global Carbon

Abstract Single carbon (C1) compounds such as methanol, methylamines and formaldehyde are ubiquitous in nature and they are large components of the carbon cycle. In anoxic environments C1-utilizing microbes (methylotrophs) play an important role in controlling global carbon degradation. Currently described anaerobic methylotrophs are limited to methanogenic archaea, acetogenic bacteria, and sulfate-reducing bacteria. Here, we report the first archaeal lineage outside of methanogenic taxa that are capable of anaerobic methylotrophy. Phylogenetic analyses suggest these archaea form a new phylum within the TACK superphylum, which we propose be named Brockarchaeota. A survey revealed Brockarchaeota are globally distributed in geothermal springs. Metabolic inference from 15 metagenome-assembled genomes from hot springs and deep-sea sediments indicates that Brockarchaeota are strict anaerobes. They contain a variety C1 metabolisms including the methanol and trimethylamine methyltransferases system, the ribulose bisphosphate pathway coupled with the non-oxidative pentoses phosphate pathway, and reductive glycine pathway. Brockarchaeota have an incomplete methyl-branch of the Wood-Ljungdahl pathway probably used for formaldehyde oxidation, since they lack several core genes involved in methanogenesis including methyl-CoM reductases. Brockarchaeota also appear to play an important role in the breakdown of plant-derived polysaccharides, especially cellulose, starch and xylan. Their broad distribution and their capacity to use both C1 compounds and complex polysaccharides via anaerobic metabolism suggest that the Brockarchaeota occupy previously overlooked roles in carbon cycling.

Adhesion of Biodegradative Anaerobic Bacteria to Solid Surfaces

1999 ◽  
Vol 65 (11) ◽  
pp. 5082-5088 ◽  
Author(s):  
Paula M. van Schie ◽  
Madilyn Fletcher
Keyword(s):  
Anaerobic Bacteria ◽  
Solid Surfaces ◽  
The Other ◽  
Strictly Anaerobic ◽  
Anoxic Environments ◽  
Syntrophomonas Wolfei ◽  
Subsurface Environments ◽  
Desulfomonile Tiedjei ◽  
Glass Surfaces

ABSTRACT In order to exploit the ability of anaerobic bacteria to degrade certain contaminants for bioremediation of polluted subsurface environments, we need to understand the mechanisms by which such bacteria partition between aqueous and solid phases, as well as the environmental conditions that influence partitioning. We studied four strictly anaerobic bacteria, Desulfomonile tiedjei,Syntrophomonas wolfei, Syntrophobacter wolinii, and Desulfovibrio sp. strain G11, which theoretically together can constitute a tetrachloroethylene- and trichloroethylene-dechlorinating consortium. Adhesion of these organisms was evaluated by microscopic determination of the numbers of cells that attached to glass coverslips exposed to cell suspensions under anaerobic conditions. We studied the effects of the growth phase of the organisms on adhesion, as well as the influence of electrostatic and hydrophobic properties of the substratum. Results indicate thatS. wolfei adheres in considerably higher numbers to glass surfaces than the other three organisms. Starvation greatly decreases adhesion of S. wolfei and Desulfovibrio sp. strain G11 but seems to have less of an effect on the adhesion of the other bacteria. The presence of Fe3+ on the substratum, which would be electropositive, significantly increased the adhesion ofS. wolfei, whereas the presence of silicon hydrophobic groups decreased the numbers of attached cells of all species. Measurements of transport of cells through hydrophobic-interaction and electrostatic-interaction columns indicated that all four species had negatively charged cell surfaces and that D. tiedjei andDesulfovibrio sp. strain G11 possessed some hydrophobic cell surface properties. These findings are an early step toward understanding the dynamic attachment of anaerobic bacteria in anoxic environments.

scholarly journals Development of a Microarray-Based Tool To Characterize Vaginal Bacterial Fluctuations and Application to a Novel Antibiotic Treatment for Bacterial Vaginosis

2015 ◽  
Vol 59 (5) ◽  
pp. 2825-2834 ◽  
Author(s):  
Federica Cruciani ◽  
Elena Biagi ◽  
Marco Severgnini ◽  
Clarissa Consolandi ◽  
Fiorella Calanni ◽  
...  
Keyword(s):  
Bacterial Vaginosis ◽  
Anaerobic Bacteria ◽  
Reproductive Age ◽  
Strictly Anaerobic ◽  
Genital Tract Infection ◽  
Content Type ◽  
Lower Genital Tract ◽  
Antimicrobial Protection ◽  
Lower Genital Tract Infection ◽  
Bacterial Groups

ABSTRACTThe healthy vaginal microbiota is generally dominated by lactobacilli that confer antimicrobial protection and play a crucial role in health. Bacterial vaginosis (BV) is the most prevalent lower genital tract infection in women in reproductive age and is characterized by a shift in the relative abundances ofLactobacillusspp. to a greater abundance of strictly anaerobic bacteria. In this study, we designed a new phylogenetic microarray-based tool (VaginArray) that includes 17 probe sets specific for the most representative bacterial groups of the human vaginal ecosystem. This tool was implemented using the ligase detection reaction-universal array (LDR-UA) approach. The entire probe set properly recognized the specific targets and showed an overall sensitivity of 6 to 12 ng per probe. The VaginArray was applied to assess the efficacy of rifaximin vaginal tablets for the treatment of BV, analyzing the vaginal bacterial communities of 22 BV-affected women treated with rifaximin vaginal tablets at a dosage of 25 mg/day for 5 days. Our results showed the ability of rifaximin to reduce the growth of various BV-related bacteria (Atopobium vaginae,Prevotella,Megasphaera,Mobiluncus, andSneathiaspp.), with the highest antibiotic susceptibility forA. vaginaeandSneathiaspp. Moreover, we observed an increase ofLactobacillus crispatuslevels in the subset of women who maintained remission after 1 month of therapy, opening new perspectives for the treatment of BV.

scholarly journals Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2642-2649 ◽  
Author(s):  
Maria V. Sizova ◽  
Paul A. Muller ◽  
David Stancyk ◽  
Nicolai S. Panikov ◽  
Manolis Mandalakis ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Sequence Similarity ◽  
Anaerobic Bacteria ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type

Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1T, ACB7T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7T grew weakly on sucrose only. The growth temperature range was 30–42 °C with optimum growth at 37 °C. Major metabolic fermentation end products of strain ACB1T were acetate and lactate; the only product of strains ACB7T and ACB8 was acetate. Major fatty acids of strain ACB1T were C14 : 0, C16 : 0, C16 : 1ω7c dimethyl aldehyde (DMA) and C18 : 1ω7c DMA. Major fatty acids of strain ACB7T were C12 : 0, C14 : 0, C16 : 0, C16 : 1ω7c and C16 : 1ω7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1T, ACB8 and ACB7T formed two separate branches within the genus Oribacterium , with 98.1–98.6 % sequence similarity to the type strain of the type species, Oribacterium sinus . Predicted DNA–DNA hybridization values between strains ACB1T, ACB8, ACB7T and O. sinus F0268 were <70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1T and ACB8, and strain ACB7T are considered to represent two distinct species of the genus Oribacterium , for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1T ( = DSM 24637T = HM-481T = ATCC BAA-2638T) and ACB7T ( = DSM 24638T = HM-482T = ATCC BAA-2639T), respectively.

scholarly journals Structural and Functional Characterization of an Electron Transfer Flavoprotein Involved in Toluene Degradation in Strictly Anaerobic Bacteria

2019 ◽  
Vol 201 (21) ◽  
Author(s):  
Marian Samuel Vogt ◽  
Karola Schühle ◽  
Sebastian Kölzer ◽  
Patrick Peschke ◽  
Nilanjan Pal Chowdhury ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Conformational Changes ◽  
Functional Characterization ◽  
Anaerobic Bacteria ◽  
Biochemical Properties ◽  
Strictly Anaerobic ◽  
Toluene Degradation ◽  
Geobacter Metallireducens ◽  
Content Type ◽  
Facultatively Anaerobic

ABSTRACT (R)-Benzylsuccinate is the characteristic initial intermediate of anaerobic toluene metabolism, which is formed by a radical-type addition of toluene to fumarate. Its further degradation proceeds by activation to the coenzyme A (CoA)-thioester and β-oxidation involving a specific (R)-2-benzylsuccinyl-CoA dehydrogenase (BbsG) affiliated with the family of acyl-CoA dehydrogenases. In this report, we present the biochemical properties of electron transfer flavoproteins (ETFs) from the strictly anaerobic toluene-degrading species Geobacter metallireducens and Desulfobacula toluolica and the facultatively anaerobic bacterium Aromatoleum aromaticum. We determined the X-ray structure of the ETF paralogue involved in toluene metabolism of G. metallireducens, revealing strong overall similarities to previously characterized ETF variants but significantly different structural properties in the hinge regions mediating conformational changes. We also show that all strictly anaerobic toluene degraders utilize one of multiple genome-encoded related ETF paralogues, which constitute a distinct clade of similar sequences in the ETF family, for β-oxidation of benzylsuccinate. In contrast, facultatively anaerobic toluene degraders contain only one ETF species, which is utilized in all β-oxidation pathways. Our phylogenetic analysis of the known sequences of the ETF family suggests that at least 36 different clades can be differentiated, which are defined either by the taxonomic group of the respective host species (e.g., clade P for Proteobacteria) or by functional specialization (e.g., clade T for anaerobic toluene degradation). IMPORTANCE This study documents the involvement of ETF in anaerobic toluene metabolism as the physiological electron acceptor for benzylsuccinyl-CoA dehydrogenase. While toluene-degrading denitrifying proteobacteria use a common ETF species, which is also used for other β-oxidation pathways, obligately anaerobic sulfate- or ferric-iron-reducing bacteria use specialized ETF paralogues for toluene degradation. Based on the structure and sequence conservation of these ETFs, they form a new clade that is only remotely related to the previously characterized members of the ETF family. An exhaustive analysis of the available sequences indicated that the protein family consists of several closely related clades of proven or potential electron-bifurcating ETF species and many deeply branching nonbifurcating clades, which either follow the host phylogeny or are affiliated according to functional criteria.

The bacterial numeration and an observation of a new syntrophic association for granular sludge

1997 ◽  
Vol 36 (6-7) ◽  
pp. 133-140 ◽  
Author(s):  
Zhu Jianrong ◽  
Hu Jicui ◽  
Gu Xiasheng
Keyword(s):  
Anaerobic Bacteria ◽  
Granular Sludge ◽  
Methanogenic Bacteria ◽  
Uasb Reactor ◽  
Two Phase ◽  
Methanogenic Activity ◽  
Syntrophic Association ◽  
Group I ◽  
Acetogenic Bacteria ◽  
Fermentative Bacteria

The bacterial numeration and microbial observation were made on granular sludge from laboratory single and two-phase UASB reactors. It was shown that the fermentative bacteria (group I), H2-producing acetogenic bacteria (group II) and methanogenic bacteria (group III) of granular sludge in single UASB reactor were 9.3 × 108−4.3 × 109, 4.3 × 107−4.3 × 108, 2.0−4.3 × 108, respectively, during the granulation process. The sludge of methanogenic reactor exhibited the similar results. That indicates there is no big difference between suspended and granular sludge, and bacterial population for three groups of anaerobic bacteria are similar. The formation of granular sludge depends mainly on the organization and arrangement of bacteria. An observation of granular sludge using electron microscope revealed that the fermentative bacteria and hydrogenotrophic methanogens existed on outer surface of granules, and aceticlastic methanogens and H2-producing acetogenic bacteria occupied the inner layer. A new syntrophic association between Methanosaeta sp. and Syntrophomonas sp. (even plus Methanobrevibacter sp.) was observed. Because Methanosaeta can effectively convert the acetate (the end product of propionate and butyrate) to methane, such a new syntrophic association is supposed to support the degradation of short fatty acids and high methanogenic activity of granular sludge. Based on structural pattern, a hypothesis on mechanism of granulation called “crystallized nuclei formation” is proposed.

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