scholarly journals Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12291
Author(s):  
Maria S. Costantini ◽  
Matthew C.I. Medeiros ◽  
Lisa H. Crampton ◽  
Floyd A. Reed
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Captive Breeding ◽  
Critically Endangered ◽  
Sampling Location ◽  
Human Populations ◽  
Rrna Gene ◽  
Important Species ◽  
Fecal Samples ◽  
Hawaiian Honeycreepers

Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.

scholarly journals Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered tropical birds

2021 ◽  
Author(s):  
Maria Sara Costantini ◽  
Matthew C I Medeiros ◽  
Lisa H Crampton ◽  
Floyd A. Reed
Keyword(s):  
Endangered Species ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Critically Endangered ◽  
Sampling Location ◽  
Human Populations ◽  
Rrna Gene ◽  
Population Declines ◽  
Important Species ◽  
Hawaiian Honeycreepers

The gut microbiome of an animal has a strong influence on the health, fitness, and behavior of its host, and is thus a critical component of the animal itself. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats have caused widespread population declines of Hawaiian honeycreepers (subfamily Carduelinae). These threats, and the environmental changes that result, can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, no previous study has explored the natural patterns of the gut microbiome of a honeycreeper species in the wild. This project used amplicon-based sequencing of the 16S rRNA gene to characterize the gut microbiome of two critically endangered species of Hawaiian honeycreepers. The two species differed significantly in both alpha and beta diversity. Intraspecific variation of the gut microbiome among individual birds was a major factor. However, small but significant differences also exist between sampling location and sexes. This baseline knowledge will help inform management decisions for these honeycreeper species both in their native habitats and in captivity.

scholarly journals The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota

2021 ◽  
Vol 9 (8) ◽  
pp. 1755
Author(s):  
Zachary McAdams ◽  
Kevin Gustafson ◽  
Aaron Ericsson
Keyword(s):  
16S Rrna ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Sodium Dodecyl ◽  
Rrna Gene ◽  
Fecal Dna ◽  
Viral Inactivation ◽  
Fecal Samples ◽  
Alpha And Beta Diversity ◽  
Microbiome Analysis

Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation.

scholarly journals Impacts of Aging and Blackcurrant Supplementation on the Gut Microbiome Profile of Female Mice (P20-031-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Sang Gil Lee ◽  
Cao Lei ◽  
Melissa Melough ◽  
Junichi Sakaki ◽  
Kendra Maas ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Health Benefits ◽  
Alpha Diversity ◽  
Young Female ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Female Mice ◽  
Aged Mice ◽  
Young Mice

Abstract Objectives Blackcurrant, an anthocyanin-rich berry, has multiple health benefits. The purpose of this study was to examine the impacts of blackcurrant supplementation and aging on gut bacterial communities in female mice. Methods Three-month and 18-month old female mice were provided standard chow diets with or without anthocyanin-rich blackcurrant extract (BC) (1% w/w) for four months. Upon study completion, fecal samples were collected directly from the animals’ colons. Microbiome DNA was extracted from the fecal samples and the V3-V4 regions of their 16S rRNA gene were amplified and sequenced using Results Taxonomic analysis showed a significantly decrease in alpha diversity in aged female mice, compared to young counterparts. BC consumption did not alter the alpha diversity in either young or aged mice compared to control diets. For beta diversity, we observed the clustering was associated with age but not diet. The phylogenic abundance analysis showed that the relative abundance of several phyla, including Firmicutes, Bacteroidetes, Cyanobacteria, Proteobacteria, and Tenericutes was higher in aged compared to young mice. Among them, the abundance of Firmicutes was downregulated by BC in the young but not the aged mice. The abundance of Bacteroidetes was increased by BC in both the young and the aged groups. Noticeably, Verrucomicrobia was the only phylum whose relative abundance was upregulated in the aged female mice compared to the young mice. Meanwhile, its relative abundance in the aged group was suppressed by BC. Interestingly, Desulfovibrio, which is the most representative sulfate-reducing genus, was detectable only in young female mice, and BC increased its relative abundance. Conclusions Our results characterized the gut microbiome compositions in young and aged female mice, and indicated that the gut microbiome of young and aged female mice responded differently to four month BC administration. Through additional research, the microbial alterations observed in this study should be further investigated to inform our understanding of the effect of BC on the gut microbiome, the possible health benefits related to these changes, and the differing effects of BC supplementation across populations. Funding Sources This study was supported by the USDA NIFA Seed Grant (#2016-67018-24492) and the University of Connecticut Foundation Esperance Funds to Dr. Ock K. Chun. We thank the National Institute on Aging for providing aged mice for the project and Just the Berries Ltd. for providing the blackcurrant extract.

scholarly journals Maternal Gut Microbiome Biodiversity in Pregnancy

2017 ◽  
Vol 35 (01) ◽  
pp. 024-030 ◽  
Author(s):  
Nitasha Ricks ◽  
Alexis Panzer ◽  
Amber Mccoy ◽  
M. Azcarate-Peril ◽  
Temitope Keku ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
White Women ◽  
Phase 1 ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Gestational Weight ◽  
Biodiversity Changes ◽  
In Pregnancy

Objective To measure maternal gut microbiome biodiversity in pregnancy. Materials and Methods In phase 1, maternal fecal samples were collected by rectal swab in 20 healthy pregnant women (14–28 weeks gestation) to measure bacterial abundance. In phase 2, fecal samples were collected from 31 women at enrollment (<20 weeks gestation, baseline) and at 36 to 39 weeks of gestation (follow-up). We assessed cluster analysis to assess bacterial community profiles at the phylum level longitudinally through pregnancy. DNA was extracted from swabs, followed by PCR of the bacterial 16s rRNA gene and multiplex high-throughput sequencing (Ion Torrent). Results In phase 1, 16 of 20 samples yielded usable data. White women (n = 10) had greater abundance of Firmicutes (23 ± 0.15 vs. 16% ± 0.75, p = 0.007) and Bacteroidetes (24 ± 0.14 vs. 19% ± 0.68, p = 0.015) compared with non-White women (n = 6). In the 11 paired specimens, Bacteroidetes increased in abundance from baseline to follow-up. Compared with women who gained weight below the median gestational weight gain (GWG, <15.4 kg), those who gained above the median GWG had increased abundance of Bacteroidetes (p = 0.02) and other phyla (p = 0.04). Conclusion Maternal microbiome biodiversity changes as pregnancy progresses and correlates with GWG.

scholarly journals Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis)

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Lijuan Yao ◽  
Xiang Li ◽  
Zutao Zhou ◽  
Deshi Shi ◽  
Zili Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Developmental Stages ◽  
Rrna Gene ◽  
Rhinopithecus Roxellana ◽  
Fecal Samples ◽  
Group 3 ◽  
Group 2 ◽  
Diverse Groups

The gut microbiota represents a source of genetic and metabolic diversity of a complex polymicrobial ecosystem within its host. To investigate age-based variations of the gut microbiota among Shennongjia golden snub-nosed monkeys (Rhinopithecus roxellana hubeiensis), we characterized the microbial species in fecal samples from 18 Shennongjia golden snub-nosed monkeys evenly pooled into 3 aged groups (Group 1, 1-3 years; Group 2, 5-8 years; Group 3, above 12 years) in Shennongjia, Hubei Province, China. Genomic DNA was extracted from fecal samples, and the 16S rRNA gene V4 region was sequenced using the Illumina high-throughput MiSeq platform PE250. A total of 28 microbial phyla were identified in the gut microbiome of these monkeys with the ten most abundant phyla (i.e., Firmicutes, Bacteroidetes, Verrucomicrobia, Spirochaetes, Tenericutes, Proteobacteria, Planctomycetes, Fibrobacteres, Cyanobacteria, and Euryarchaeota). A total of 1,469 (of 16 phyla and 166 genera), 1,381 (of 16 phyla and 157 genera), and 1,931 (of 19 phyla and 190 genera) operational taxonomic units (OTUs) were revealed in Groups 1, 2, and 3, respectively, with Group 3 containing the most diverse groups of OTUs as revealed by the species relative abundance clustering analysis. These results suggest that the gut microbiota in these monkeys maintain a dynamic status, starting from the early developmental stages of life with the species relative abundance increasing with age. This is the first study to comprehensively characterize the gut microbiota and provide valuable information for monitoring the health and nutritional needs of this endangered primate at different ages.

scholarly journals PSII-24 Towards a better understanding of the gut microbiome functions in the swine production: extensive cultivation of the swine gut microbiome from different growth stages

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 242-243
Author(s):  
Xiaofan Wang ◽  
Xiaoyuan Wei ◽  
Feilong Deng ◽  
Tsungcheng Tsai ◽  
Charles V Maxwell ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Pathogenic Bacteria ◽  
Illumina Miseq ◽  
Positive Control ◽  
Growth Stages ◽  
Rrna Gene ◽  
Swine Production ◽  
Fecal Samples ◽  
Different Growth Stages

Abstract Substantial progress has been made in the culture-omics of the human gut microbiota. However, little is known about the culture-omics of the swine gut microbiota, despite recent reports of their significant roles in swine health and production. To fill this knowledge gap in research, we tested 52 bacterial cultivation methods with different media and gas combinations. Fresh fecal samples (0.2g/sample) were collected from three pigs at the end of four growth stages: lactation, nursery, growing and finishing and were mixed with a stomacher in 20 mL saline. Aliquots of 50 uL microbial suspensions were then spread onto different media plates and incubated under aerobic and anaerobic conditions at 37C for up to 5 days. An additional aliquot of each sample was subjected to direct DNA extraction as a positive control. Bacterial colonies from each plate were collected and DNA was extracted from these samples using the Powersoil DNA isolation kit and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 378, 482, 565, and 555 bacterial features were observed from microbial solutions at the end of lactation, nursery, growing and finishing. Our culturing methods recovered 415, 675, 808, and 823 features correspondingly, representing 45.2%, 54.8%, 53.3%, and 56.4% of total features observed in microbial solutions. The top ten most easily cultured genus were Escherichia, Streptococcus, Lactobacillus, Megasphaera, Acidaminococcus, Bacillus, Mitsuokella, Enterococcus and Prevotella. Non-parametric permutational multivariate analysis of variance shows that the main factors driving the swine culture-omics included medium, age and oxygen condition. This study identifies the cultivable bacteria from fecal samples collected at different growth stages of pigs and provides a guidance to cultivate potential beneficial or pathogenic bacteria of interests and validate their functions in swine production.

scholarly journals Destabilization of The Bacterial Interactome Tracks Nutrient Restriction-Induced Dysbiosis in Insect Gut

2020 ◽  
Author(s):  
Ramona Marasco ◽  
Marco Fusi ◽  
Matteo Callegari ◽  
Costanza Juker ◽  
Francesca Mapelli ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Growth And Development ◽  
16S Rrna Gene Sequencing ◽  
Nutrient Restriction ◽  
Rrna Gene ◽  
Insect Growth ◽  
Biotic Stresses ◽  
Polyphagous Insect ◽  
Insect Gut

Abstract Background. Stress affects host growth and development and can induce changes in the gut microbiome, commonly defined as dysbiosis. Dysbiosis has been proposed to affect community beta-diversity and within-beta-diversity (community dispersion). As abiotic and biotic stresses, nutrient restriction (NR) also impairs host fitness and results in dysbiosis. However, NR does not introduce overt negative effectors or selectors, such as toxic compounds, pathogens, or parasites, resulting in its role as a determinant of beta-diversity changes being questioned. We hypothesize that following NR, gut dysbiosis is reflected via changes in networking properties of the microbiome rather than via variation in its beta-diversity and/or dispersion. To test our hypothesis, we fed the black soldier fly, Hermetia illucens, a nutritionally versatile polyphagous insect, with two NR diets and a control full-nutrient (FN) diet. Then, we assessed the effects of NR on insect growth and development and gut physicochemical conditions to validate the presence of dysbiosis. In addition, we analyzed the bacterial diversity associated with larvae, pupae, and adults via 16S rRNA gene sequencing to assess the role of NR on the composition, structure, and stability of the bacterial communities.Results. NR strongly affected insect growth and development, inducing significant changes in the physiochemical conditions of the larval gut. Further, diet-dependent differences in bacterial composition—expected in holometabolous/polyphagous insects—were observed, with enrichment in diet-specific keystone bacterial taxa (Bacilli in FN-fed individuals and Clostridia and Gamma- and Alphaproteobacteria in NR-fed individuals), and greater microbiome dispersion in adults but not in larvae and pupae.Conclusions. While NR establishes alternative stable configurations of the gut microbiome compared with normally fed gut, NR-driven dysbiotic growth performance is considerably reflected in rarefied, less structured, and connected bacterial interactomes than in within beta-diversity changes.

scholarly journals Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sandra A. Appiah ◽  
Christine L. Foxx ◽  
Dominik Langgartner ◽  
Annette Palmer ◽  
Cristian A. Zambrano ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Composition ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Global Changes ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Increased Risk

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

scholarly journals The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wen Wang ◽  
Xiaolong Gao ◽  
Sisi Zheng ◽  
Zhuoma Lancuo ◽  
Ying Li ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Pathogenic Bacteria ◽  
Feeding Habits ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Diversity ◽  
Protective Role ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Fecal Samples

Abstract Background Himalayan Griffons (Gyps himalayensis), large scavenging raptors widely distributed in Qinghai-Tibetan Plateau, have evolved a remarkable ability to feed on carcasses without suffering any adverse effects. The gut microbiome plays an important role in animal physiological and pathological processes, and has also been found to play a health protective role in the vulture adaptation to scavenging. However, the microbial taxonomic diversity (including nonculturable and culturable microbes), functions, and metabolites related to Himalayan Griffons have not been fully explored. Methods In the present study, the 28 fecal samples of the Himalayan Griffons and 8 carrion samples were collected and sequenced using high-throughput 16S rRNA gene sequencing methods to analyze the composition and functional structures of the microbiomes. Twelve fecal samples of the Himalayan Griffons were analyzed using untargeted Liquid Chromatography Mass Spectroscopy (LC–MS) to identify metabolites. We used different culture conditions to grow Himalayan Griffons gut microbes. Inhibitory effects of gut beneficial bacteria on 5 common pathogenic bacteria were also tested using the Oxford cup method. Results According to the results of the culture-independent method, a high abundance of four major phyla in Himalayan Griffons were identified, including Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. The most abundant genera were Fusobacterium, followed by Clostridium_sensu_stricto_1, Cetobacterium, Epulopiscium, and Bacteroides. The predicted primary functional categories of the Himalayan Griffons’ gut microbiome were associated with carbohydrate and amino acid metabolism, replication and repair, and membrane transport. LC–MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples. Cultivation yielded 184 bacterial isolates with Escherichia coli, Enterococcus faecium, Enterococcus hirae, and Paeniclostridium sordellii as most common isolates. Moreover, 7 potential beneficial gut bacteria isolated showed certain inhibition to 5 common pathogenic bacteria. Conclusions Our findings broaden and deepen the understanding of Himalayan Griffons’ gut microbiome, and highlighted the importance of gut microbiome-mediated adaptation to scavenging habits. In particular, our results highlighted the protective role of gut beneficial bacteria in the Himalayan Griffons against pathogenic bacteria that appear in rotten food resources.

scholarly journals Sewage Reflects the Microbiomes of Human Populations

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Ryan J. Newton ◽  
Sandra L. McLellan ◽  
Deborah K. Dila ◽  
Joseph H. Vineis ◽  
Hilary G. Morrison ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Marker Gene ◽  
Population Variation ◽  
Human Populations ◽  
Rrna Gene ◽  
Community Structures ◽  
Data Set ◽  
Stool Samples ◽  
Number Of Individuals

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. IMPORTANCE The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.

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