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High levels may cause constipation and digestion issues while low levels may lead to reduce anti-inflammatory gut activities . [12] study data from the Russian Metagenome Project website (http://www.metagenome.ru/files/rus_met/). Save time on interpreting lab results with the largest database of biomarkers online. Two of these taxa were found in only one sample, and all of the others were identified in only populations from one study (the European samples from the Arumugam study). UK Bacteroides species surveillance survey: Change in antimicrobial resistance over 16 years (2000-2016). . The ellipses in Figs. The gut microbiomes of Americans and Europeans having a Western diet tend to be dominated by Bacteroides and Clostridiales, while rural populations with a high fiber, low-protein diet tend to be dominated by Prevotella. Comment: Although resistance has been previously described to both MTZ and carbapenems in B. thetaiotaomicron, this is the first report in which an isolate is resistant to both. Samples are colored by most prominent taxon in the original samples distributions (same as in plot A). Enter your email below and we'll resend your username to you. Gastroenterol. The immune response to Prevotella bacteria in chronic inflammatory Bacteroides,Prevotella, and other groups, however it is challenging to separate many of the species. ", Kobayashi, T., & Auwaerter, P. G. (2021). What Is the Pathogenesis of Bacteroides Infection? Prevotella ratio distributions (relative abundance of Prevotella/[Bacteroides+Prevotella]) within each population. This drug is often thought of as the equivalent of cefoxitin but with longer dosing intervals. The dearth of any consistent features of these communities across independent studies is a reminder for us not to extrapolate from PCoA and NMDS plots to assumptions about the defining characteristics of the entire communities. Biomarkers serve as a measurable indicator of a biological state or environmental exposure [21]. Logistic and linear regression models were used to associate the binary and continuous factors with the community types using the glm and lm functions. The x-axis represents quantiles (from 0 to 1) to facilitate simultaneous plotting. Fusobacterium has also been associated with colon cancer [24]. No correlations were found within the Prevotella-dominated samples in more than one previous study. that two of the three clusters were not distinct. When colored by population, we see that the second axis separates the samples within a population, as does the first axis but to a lesser extent (Fig. Google Scholar, Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK et al. About 18.5% of the isolates were . Thousands of dead fish washed up on this Texas beach. What happened? Prevotella | Johns Hopkins ABX Guide - Hopkins Guides doi:10.1126/science.1208344. 1a and 1d were constructed as confidence regions for each of the groups; these regions would represent 95% of the points if the bivariate data were Gaussian. No longer available in the U.S. market. Interestingly, there is still clustering structure and differentiation of samples visible in Fig. This Prevotella ratio provides a continuous variable for measuring the spectrum of abundance values, rather than a binary value representing only the dominant taxon. The abundance of the two high-taxonomic rank microbe groups is significantly associated with irAEs. Both populations included a few subjects dominated by Actinobacteria, mainly Bifidobacterium, a beneficial microbe associated with milk-based diets such as breast-feeding [9]. b Samples are colored by their value for the Prevotella ratio (relative abundance of Prevotella/[Bacteroides+Prevotella]) on a spectrum with red indicating no Prevotella and purple no Bacteroides. PubMed Karlowsky JA, Walkty AJ, Adam HJ, et al. Kobayashi T, Auwaerter PG. Unfortunately, relative abundance data are not statistically sufficient to accurately assess internal microbiome interactions [18], but as several of the studies only provided these proportions and not the original read numbers, we proceeded using relative abundance and took several precautions to avoid the biases this can induce. A Johns Hopkins Guides subscription is required to, Obligate anaerobes, but among the most aerotolerant, Reports of higher carbapenem resistance rates reported from Taiwan (7-12%), Germany (4.9-5.3%) and Canada (2.3-12.7%). Type your tag names separated by a space and hit enter. Whether distinct community types or gradients, stable over time or not, we do not have a functional description of what other bacteria comprise the Prevotella- or Bacteroides/Clostridiales-dominated clusters beyond the dominant taxon. Four bacteria are enriched with aspirin use versus no medication and includes Bacteroides spp., Prevotella spp., Barnesiella spp. Comment: Authors now state that in the UK, anaerobic susceptibility testing should be routine. Proceedings of the Royal Society of London. The nitroimidazole class is the most potent antibiotic available for anaerobic bacterial infection. Anastassia Gorvitovskaia is a senior at Brown University working towards a Bachelor of Science in Computational Biology. Tigecycline 3.9 to 14.6%. Thousands of dead fish were found laying on beaches in Quintana Beach County Park early Friday, leaving beachgoers alarmed and . Virtually all members of the genus are sensitive to. That means junk food like processed carbohydrates, AS WELL AS complex carbohydrates like high fiber diets have been shown to create Prevotella abundance. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species . Springer Nature. ER -, Your free 1 year of online access expired. https://doi.org/10.1038/nrgastro.2016.4, DOI: https://doi.org/10.1038/nrgastro.2016.4. Only one of datasets showed clear separation between the Bacteroides- and Clostridiales-dominated samples, while two showed overlapping points consistent with a gradient. Article http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html. (PDF 4kb). Genome Research. Metronidazole remained effective with only 2.4% resistance by the nim gene in the B. fragilis cohort, but this represented a 6x increase and the most remarkable rise of any antimicrobial tested. This is a rational single agent for treating intra-abdominal sepsis of community-onset or low severity. Wu et al. Percent susceptibility to cefoxitin, clindamycin, and moxifloxacin was lowest for B. thetaiotaomicron (n = 49, 24.5%), Parabacteroides distasonis/P. Tyakht AV, Alexeev DG, Popenko AS, Kostryukova ES, Govorun VM. It would not use as monotherapy in severe infections because many coliforms and all P. aeruginosa are resistant, along with rising rates of resistance among anaerobes. in race walkers. These ordination results show that the primary axes continue to correlate with Bacteroides and Prevotella when the studies are combined. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the enterotypes hypothesis. Enter your username below and we'll send you an email explaining how to change your password. [16] found that the ratio of the logarithm of Prevotella to Bacteroides abundance generated a natural and distinct split between Prevotella- and Bacteroides-dominated microbial communities in their samples caused by the bimodal Prevotella distribution [5]. Alauzet C, Lozniewski A, Marchandin H. Metronidazole resistance and nim genes in anaerobes: A review. We gratefully acknowledge Stephen OKeefe for having shared data tables from his study on cancer in rural Africans and African Americans with us and the Richard Fox of the Josephine Bay Paul Center at the Marine Biological Laboratory for providing computational systems support. PLoS Comput Biol. We chose instead to simply define Prevotella-dominated and Bacteroides-dominated samples as any sample in which either Prevotella or Bacteroides was the most abundant taxon. doi:10.1098/rspl.1896.0076. Your privacy choices/Manage cookies we use in the preference centre. Exploration of bacterial community classes in major human habitats. c Samples are colored by population of origin. Although common in the gut microbiome, if found elsewhere, they may be a sign of trouble or infection. A) Samples colored by their most prominent taxon. doi:10.1073/pnas.1005963107. - Displays flexibility to adapt to many environmental conditions/diets Bacteroidesconsist of bile-tolerant organismsand has the capability of Bacteroides fragilis: This gram-negative bacteria is important for microbial balance and neuroimmune health. Resistance among B. fragilis may be up to > 35%. To assess the persistent clustering of the microbial communities independent of the relative abundances of Bacteroides and Prevotella, we removed these two taxa from all the samples and reran the PCoA analysis (Fig. The first such study by Wu et al. Open Access articles citing this article. The wealth of data now available regarding human microbiota composition across populations shows that, on the whole, the most abundant bacteria in the human gut belong to two phyla, the Firmicutes and the Bacteroidetes. Comment: The microbiology of hundreds of trauma patients was examined. D) The Bray distance has been recalculated without the relative abundances of Bacteroides and Prevotella. SPH was funded by NIH R01 GM099534. Vienna, Austria: R Foundation for Statistical Computing; 2012. There's more to see -- the rest of this topic is available only to subscribers. BT - Johns Hopkins ABX Guide Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Across the studies, Prevotella was associated with non-Western, rural communities, and a plant-based diet rich in polysaccharides and fiber [2, 8, 10, 11, 13, 21]. ", Auwaerter, P. G. (2022). - Along with Methanobrevibacter smithii, certain Clostridium and Bacteroides spp. PubMed AG helped with the design of the study, carried out the statistical analysis of the data, and drafted the manuscript. Recent evolution of antibiotic resistance in the anaerobes as compared to previous decades. Their reanalysis of the data, using OTUs (which they referred to as species-level), reproduced the results of the source publications. The genera represented in the taxonomy tables were filtered to include only genera whose maximum relative abundance across all samples was greater than 0.0001 or 0.01%. Bacteroides species | Johns Hopkins ABX Guide The predominant anaerobic bacteria included Bacteroides spp., Peptostreptococcus spp, Clostridium spp), Prevotella spp, and Fusobacterium spp. Our technology helps to understand, combine, track, organize, and act on your medical lab test results. Enterotypes of the human gut microbiome. In 2015, papers probed the genomic diversity of Prevotella strains and interactions of Prevotella copri with its host and other bacteria. Google Scholar. The reads were assigned taxonomy by comparison against the SILVA database [26] using GAST [27]. Each dataset independently displayed a similar clustering pattern with subjects dominated by one of three different taxa: Bacteroides, Provetella, or members of the order Clostridiales. The number of DNA reads returned by next-generation sequencing for a bacterial sample does not reflect the absolute abundance of bacteria in the original sample. The correlations were run on the Prevotella-dominated and Bacteroides-dominated samples for each individual study independently and then on the compiled group of all studies. Enterotypes of the human gut microbiome. (PDF 28kb), Prevotella distributions within each population. Despite the frequent use of the term enterotype to describe clustering of the gut microbiomes of research subjects from different cultures and with different dietary habits, the membership of the microbial communities associated with the enterotypes has not been clearly defined. Accetto, T. & Avgutin, G. Polysaccharide utilization locus and CAZYme genome repertoires reveal diverse ecological adaptation of Prevotella species. In the meantime, to ensure continued support, we are displaying the site without styles After the creation of the genus Prevotella and reclassification of moderately saccharolytic Bacteroides as Prevotella species by Shah and Collins . http://www.nature.com/nature/journal/v505/n7484/full/nature12820.html. doi:10.1128/aem.03549-13. Most are reported in Bacteroides fragilis group. 2=0.73), but neither of these had a significant correlation in any single study. Comment: A study from India found that MTZ-resistant strains were found in 3 non-B. The gene sequence is markedly different from those of other bacterial leukotoxins. MICROBIOLOGY Non-motile Gram-negative bacillus; may appear as slender rods or coccobacilli. Over the course of their genetic differentiation they seem to have divvied up the niches. D) The Bray distance has been recalculated without the relative abundances of Bacteroides and Prevotella. 2012;10(9):5912. Leukotoxin has been sequenced and shown to encode a protein of 3241 amino acids (Narayanan et al., 2001). Prevotella in the gut: choose carefully | Nature Reviews Cell Rep. 11, 527538 (2015). Genome Biol. Rethinking Enterotypes. Google Scholar. Yatsunenko et al. Frontiers | Evaluating the clinical relevance of the enterotypes in the Because Prevotella and Bacteroides have the greatest range of values and tend to be inversely related, they contribute the most to the magnitude of pairwise distances, and therefore contribute the most to separation in ordination plots, leading to Bacteroides- and Prevotella-dominated gradients in ordination plots. AG was funded by a Summer Research Assistantship grant for summer 2014. It is unlikely that there will be any new agent in another class in the foreseeable future that can challenge metronidazole in terms of in vitro activity, bactericidal activity, or in vivo results. Article Prevalence of antimicrobial resistance among clinical isolates of Bacteroides fragilis group in Canada in 2010-2011: CANWARD surveillance study. At the genus level, Bacteroides, Escherichia, and Prevotella contributed to the majority of the human gut microbiota, with an average prevalence of 36.52%, 16.03%, and 9.84%, respectively (Fig. This is a reasonably good drug for B. fragilis. Prevotella diversity, niches and interactions with the human host - Nature 1) and include the NMDS plots in the Additional files 12 and 13 (Figures S6 and S8 show the screeplots of the eigenvalues/percentage of variances explained). Easily cultivated Clinically significant species: B. fragilis, B. thetaiotaomicron, B. vulgatus, B. distasonis, B. ovatus, B. uniformis, B. caccae. (PDF 17kb), PCoA plots using the Bray distance metric with only the Yatsunenko study. Bacteroides-Prevotella group | Healthmatters.io If the sample is dominated neither by Prevotella nor Bacteroides, it is classified as other. Our internal code of conduct adds additional privacy protection. - Tart cherry juicemay normalize high or low levels. The US subjects clustered separately from the Malawian and Venezuelans, who had relatively more Prevotella. AU - Auwaerter,Paul,M.D. DB - Johns Hopkins Guides We compared the abundance distributions of Prevotella and Bacteroides with other common genera in the combined studies (Fig. This file contains all the code the reader could require to follow the same workflow on a different data set. Nature 473: 174-180 doi:10.1038/nature09944. Trosvik P, de Muinck EJ. To confirm this finding of no consistent multi-study taxa associated with either dominant taxon, and to increase our statistical power of detection, we combined the samples from all of the studies and reanalyzed them. In. Results Here we analyze the combined microbiome data of five earlier studies and show that the gut microbiomes labeled as Bacteroides and Prevotella enterotypes do not represent consistent or predictable communities. doi:10.1371/journal.pcbi.1003531. For the proportionality analysis, the Lovell et al. Microbiome Enter your email below and we'll resend your username to you. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden. The native African diet was high in complex fiber, while the African American diet was a Western diet high in protein. Active against many all anaerobes, most streptococci, and coliforms, but resistance rising and has less than optimal activity against many P. aeruginosa. Bacteroides species. We propose that the dominant taxa associated with the original enterotypes hypothesis, Bacteroides and Prevotella, as well as other taxa such as Bifidobacterium, Fusobacterium, and various Clostridiales genera, are more accurately understood as biomarkers. study, the pink points are from the Malawi, Venezuela, US Yatsunenko et al. 1c), or by their Prevotella ratio (defined above) (Fig. fragilis of total Bacteroides spp. While the original study included a correlation analysis, the results represented the differences in their particular study populations, rather than a set of universal correlations. In Western populations it has been associated with diets rich in fruits and vegetables. What is Prevotella spp.? High and low values - Healthmatters 1a, b and c and Figure S5ABC. Furthermore, Bacteroidesspp. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. 20002023 Unbound Medicine, Inc. All rights reserved, TY - ELEC Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. In fact, only Faecalibacterium and Enterobacteriaceae appear in even two of the four studies that reported correlation analyses. The ingredients of the diet eaten by the metropolitan subjects were similar to those in a Western diet, but the sources of their food were very different. PubMedGoogle Scholar. The green points are from the Native African vs. African American Ou et al. About 73.3% of the isolates were non-susceptible to penicillin, mainly due to high resistance rates in the Bacteroides spp. Resistance rates in Bacteroides described with reduced susceptibilities in Greece (11.7%) and Pakistan (16%) among the highest yet described. 2008;4(11):e1000255. 2010;107(33):146916. 2014;80(3):11429. Firmicutes as a phylum, however, is unlikely to be an effective candidate for a biomarker, as it incorporates a diversity of genera. Correspondence to PLoS Comput Biol. Exception: most tuboovarian abscesses, some. The many correlative studies of the gut microbiome and associations with diet, environment, and disease can be made more useful by moving beyond basic ordination plots to rigorously assessing their sensitivity and specificity as biomarkers of lifestyle and disease in clinical subpopulations. Human gut microbiome viewed across age and geography. Tibetans living at 4800 m have a flora . The DESeq2 analysis confirmed the previous analyses, showing no taxa consistently associating with the Bacteroides- and Prevotella-dominated samples. fragilis groups at 25.4% resistance. Friedman J, Alm EJ. Background/objectives: Individuals with high pre-treatment bacterial Prevotella-to-Bacteroides (P/B) ratio have been reported to lose more body weight on diets high in fiber than subjects with a low P/B ratio. Comment: In a study of 24 healthy adults given clindamycin with probiotic yogurt with or without the above-described bacteria, the probiotic preparation prevented the outgrowth of Bacteroides spp. We downloaded the Human Microbiome Project (HMP) data from the VAMPS website [28] at the Marine Biological Laboratory (https://vamps.mbl.edu) under the name HMP_ST_v3v5. This is the first major B. fragilis drug with extensive trials in the 1970s. Dr. Myhill mentions Ursodeoxycholic acid. - Increased in obese adolescents who lost more than 4 kg on a calorie-restricted diet, - Increased in overweight men drinking low glycinin soymilk compared to regular soymilk or bovine milk. Gut Microbes 5, 562570 (2014). Frontiers | Strenuous Physical Training, Physical Fitness, Body Oropharyngeal flora predominated in infections originating from head and neck wounds, abscesses; bites); GI flora in peritonitis, intra-abd abscesses, decubiti. (PDF 16kb), Relative variances explained by the PCoA axes from the PCoA analyses. (ZIP 11504kb), Bacteroides distributions within each population. Prevotella [Internet]. BUSINESS, ECONOMY & LABOR. Privacy Prevotella is associated with plant-rich diets (high levels of complex carbohydrates and fruit and vegetable intake), whereas Bacteroides is linked to a high intake of fat and protein. Bacteroides may be passed from mother to child during vaginal birth and thus become part of the human flora in the earliest stages of life ().The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, and their role as commensals has been extensively reviewed ().A quote in a recent publication captured this attribute: "with B. fragilis . Susan P. Holmes. Clindamycin was the worst performer in the non-B. D) The Bray distance has been recalculated without the relative abundances of Bacteroides and Prevotella. B) Samples are colored by their value for the Prevotella ratio (relative abundance of Prevotella/[Bacteroides+Prevotella]) on a spectrum with red indicating no Prevotella and purple no Bacteroides. [6] further cautioned that supervised ordination methods can lead to false clustering when the number of features in the data (here microbial genera) is much higher than the number of samples, as is the case in most human gut microbiome studies. 1. Of all the taxa in the combined studies, Bacteroides and Prevotella are the only two whose relative abundances frequently exceed 40% (Fig. volume13,pages 6970 (2016)Cite this article. It has no against Pseudomonas or many nosocomial Enterococcus infections. PubMed B) Relative variances explained by the PCoA axes used in the adjusted sample plot in Additional file 7: Figure S7D, which had its Bacteroides and Prevotella relative abundances removed. Article All data is backed up multiple times a day and encrypted using SSL certificates. That said, resistance is not wholly related to the nim genes, so other factors likely. Overall rates of percent susceptibility were as follows: 99.7%, metronidazole; 99.5%, piperacillin-tazobactam; 99.2%, imipenem; 97.7%, ertapenem; 92.0%, doripenem; 87.3%, amoxicillin-clavulanate; 80.9%, tigecycline; 65.9%, cefoxitin; 55.6%, moxifloxacin; and 52.2%, clindamycin. Ou et al. 16, 82 (2015). Multidrug-Resistant Bacteroides fragilis Seattle, Washington, 2013 36:343-347, 1992), rates of resistance have increased for amoxicillin-clavulanate, from 0.8% (1992) to 6.2% (2010-2011), and for clindamycin, from 9% (1992) to 34.1% (2010-2011). Sadarangani SP, Cunningham SA, Jeraldo PR, et al. - Generally associated with industrialized populations consuming a Western diet. Auwaerter PG. We propose the use of biomarker as a more accurate description of these and other taxa that correlate with diet, lifestyle, and disease state. Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, et al. Lana Ferguson. 2013;41(D1):D590D6. 2010;18(7):298307. PLoS One. As part of our own analysis of over 200 healthy American subjects enrolled in the Human Microbiome Project (HMP) [3], we confirmed the results of Wu et al. This is a preview of subscription content, access via your institution. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The green points are from the Native African vs. African American Ou et al. The black line represents all the samples scaled together on the x-axis. - A high beef diet was associated with increases in Bacteroidesfragilis, B. vulgatusand Clostridium spp. carried out . The in vitro data for activity vs. B. fragilis is similar to moxifloxacin, but the published clinical experience is less. Nature Reviews Gastroenterology & Hepatology was seen with other medications including NSAIDs with PPIs, and NSAIDs with antidepressants and laxatives. 2012;22(2):2928. 12, 1425 (2015), Ley, R. Prevotella in the gut: choose carefully. B) Same MDS plot as in A, but with samples colored based on their value for the Prevotella ratio on a spectrum with red indicating no Prevotella and purple no Bacteroides. You are using a browser version with limited support for CSS. De Filippis, F. et al. 1. Bacteroides Infection Treatment & Management Updated: Oct 27, 2022 Author: Itzhak Brook, MD, MSc; Chief Editor: Michael Stuart Bronze, MD more. The Prevotella ecosystem contains a lot of microbes that like to dine on proteins in. http://dx.doi.org/10.4161/gmic.28685. In 2011, Arumugam et al. Huse SM, Ye Y, Zhou Y, Fodor AA. Martnez, I. et al. If the sample is dominated neither by Prevotella nor Bacteroides, it is classified as other. [2] graphically illustrated correlations between Bacteroides and dietary amino acids and fats. Certain opportunistic pathogenic bacteria, such as Bacteroides caccae, Bacteroides massiliensis, and Bacteroides vulgatus, are higher in abundance in individuals with GDM and T2D suggesting that these bacteria may play a role in the development of hyperglycemia associated with these conditions [67, 68]. If the sample is dominated neither by Prevotella nor Bacteroides, it is classified as other. Dillon, S. M. et al. Rev. Samples high in Bacteroides or members of the order Clostridiales, including Ruminococcus, form a continuum, rather than discrete clusters. [. Bacteroides and Prevotella are gram-negative anaerobic bacteria found mainly in the gut of humans. 1a) and the Prevotella ratio (the ratio of Prevotella to the sum of Prevotella and Bacteroides) (Fig. (99.2%) and Prevotella spp. Article Bacteroides and Prevotella species have their own specific habitats in the human body as they are antagonistic. Upload your lab report and well interpret and provide you with recomendations today. Zhu, A., Sunagawa, S., Mende, D. & Bork, P. Inter-individual differences in the gene content of human gut bacterial species. Comment: The first described resistance, the nim gene, in Bacteroides now with 11 nim genes known (nimA to nimK). PubMed Google Scholar. Gut http://dx.doi.org/10.1136/gutjnl-2015-309957 (2015). Nat Commun. According to a 2007 study published in Clinical Microbiology Review, they have the most antibiotic resistance . UR - https://www.hopkinsguides.com/hopkins/view/Johns_Hopkins_ABX_Guide/540705/all/Prevotella Antimicrobial susceptibilities: B. fragilis is the most commonly resistant organism, with low rates of resistance (1-2% range) in the U.S. and Europe. Get the most important science stories of the day, free in your inbox. Prevotella increases have been associated with high-fiber, plant-based diets and non-industrialized populations, while Bacteroides increases were linked to Westernized populations with diets rich . None of these associations, however, were apparent across all studies. Medical Care The patient's recovery from. study, the yellow points are from the Russian Urban vs Rural Tyakht et al. Lassmann B, Gustafson DR, Wood CM, et al. 1d and Figure S5D, which had its Bacteroides and Prevotella relative abundances removed. Lozupone, C. A. et al. To illustrate the impact of the dominant taxon on the ordination of the microbial communities, we removed both Prevotella and Bacteroides rows in all the data and reran the ordination, without rescaling, to illustrate the change in separation (Fig. study, the yellow points are from the Russian Urban vs Rural Tyakht et al. While the Prevotella-dominated samples did cluster separately with the HMP data, we speculated that as more samples and studies were evaluated, the separation between clusters would diminish, and gut communities would appear as a continuum of abundance gradients between Bacteroides, Prevotella, and various members of the order Clostridiales.

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