Microbiol. The pathway ID ko00480 of the glutathione metabolism had an increase in abundance from before treatment to after treatment. The https:// ensures that you are connecting to the In total, the FMD gut microbiota was classified into 144 phyla, 109 classes, 230 orders, 496 families, 1913 genera, and 9041 species. Objectives: We aimed to test the hypothesis . The clinical symptoms shown are that the uric acid cannot be lowered and the siltation of the joint cavity of patient is getting more and more serious. Gut microbiome pattern reflects healthy aging and predicts survival in humans. CAS We conducted a metagenome-wide shotgun sequencing analysis of gut microbiota and measured the TMAO levels in plasma of 22 HF patients during the compensated phase and 11 age-, sex-, and comorbidity-matched control subjects, whose gut microbiota compositions were reported in a previous 16S rRNA-based analysis. BLAST comparisons of all sequences yielded 62,036 hits to the COG database, corresponding to 2407 unique COGs. Khanna, S. et al. Using metagenomic sequencing analysis, we established a distinct signature associated with chronotype based on two bacterial genera, Alistipes (elevated in "larks") and Lachnospira (elevated in "owls"). Dubourg, G. et al. Rev. Dis. The site is secure. If the patient with gout does not take the medicine during the acute onset period, it will definitely not get better in 2 weeks. National Library of Medicine itag sequencing analysis revealed strong differences in bacterial community structure already at the phylum level, both between the Compared to 16S analysis, metagenomics analysis could find that the intestinal microbiota of gout patients was highly distinct from healthy individuals in both organismal and functional structures, even build up a diagnosis model as a possible future application approach, higher than the blood-uric-acid based approach [22]. NIHMS262982-supplement-Supplementary_Online_Materials.pdf, http://gordonlab.wustl.edu/supplemental/Gill/Msmithii/draftgenome/, http://gordonlab.wustl.edu/supplemental/Gill. Rev. Only one archaeal phylotype was identified (i.e., M. smithii). Google Scholar. Alang, N. & Kelly, C. R. Weight Gain After Fecal Microbiota Transplantation. 30 patients with gout and 29 matched controls were recruited of which 16 patients took H treatment and 14 patients took T treatment. Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation, http://creativecommons.org/licenses/by/4.0/, Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Future studies are needed to provide deeper coverage of the microbiome and to assess the effects of age, diet, and pathologic states (e.g., inflammatory bowel diseases, obesity, and cancer) on the distal gut microbiome of humans living in different environments. Gigascience 8 (2019). If you are an author contributing to an RSC publication, you do not need to request permission Alignments of the reads to the draft genome of M. smithii exhibit a much narrower range of percent identity (89% of alignments were at 95% or better identity as compared with 48% for B. longum), consistent with lower levels of diversity among archaeal members of the gastrointestinal tract. When the gout patient has a single joint inflammation reaction during the acute attack (gout attack), such as severe pain in the big toe [5], treatment is required to ensure the reduction or disappearance of the acute symptoms. Firmicutes and Actinobacteria were less common in the CDI group (respectively 33.5% and 1.4%) compared to the control group (respectively 55.2% and 14.3%). 2). Li R., Yu K., Li C. Dietary factors and risk of gout and hyperuricemia: a meta-analysis and systematic review. As for Bacteroidetes, it decreased from group A_down to group B_down and increased from group B_down to group Con (Figure 6). Bethesda, MD 20894, Web Policies Our study involved 19 stool samples divided in two groups: one CDI group and one control group. Moreover, five bacteria (Fig. Metagenomic and Metabolomic Analysis of the Structure and Function of the Human Gut Microbiome in Congenital Heart. Each pure colony obtained after subculture was identified using Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS)41. Emergence of Clostridium difficile tcdC variant 078 in Marseille, France. Before The human gut microbiome is enriched for genes involved in starch and sucrose metabolism (fig. The .gov means its official. Firmicutes are implicated in butyrate and short chain fatty acid production, this molecules play a role in gut homeostasis and inhibition of C. difficile germination25,27. To delineate how the human distal gut microbiome endows us with physiological properties that we have not had to evolve on our own, we explored the metabolic potential of the microbiota in subjects 7 and 8 using KEGG (Kyoto Encyclopedia of Genes and Genomes, version 37) pathways and COGs (Clusters of Orthologous Groups) (15, 16). (B) Percent identity plot (PIP) of the alignment of shotgun reads along the draft genome of M. smithii. However, the composition, functional capacity, and metabolites of the gut microbiome about atherosclerosis have not been comprehensively studied. S1A). 2020 Sep 16;11:574500. doi: 10.3389/fimmu.2020.574500. Eur. Google Scholar. This relative paucity of Bacteroidetes sequences is in conflict with data from other studies (2, 3). Bars above both dashed lines indicate enrichment, and bars below both lines indicate underrepresentation (P < 0.05). [24] to generate the gene abundance profile. PMC legacy view Metagenomic and culturomic analysis of gut microbiota dysbiosis during, https://doi.org/10.1038/s41598-019-49189-8. 2C). The human gut microbiome is a reservoir of 10-100 trillion microorganisms that play a vital role in human health through their involvement in metabolic interactions (e.g. J. Clin. Provided by the Springer Nature SharedIt content-sharing initiative. Front Immunol. (4) Table S1. J. Med. official website and that any information you provide is encrypted However, there was also a strange phenomenon that Klebsiella increased in the intestines of patients after treatment with drugs, whether it was because of the effect of the drug or because of the decreased abundance of other bacteria, needs to be further studied. Scientific Reports (Sci Rep) Med. Studies have shown that during the development of gout, the closely related monosodium urate (MSU) crystals can affect the production of certain immune cells, cytokines, and effector molecule expression, triggering both innate and adaptive immune responses [10]. 5 (2017). Open Forum Infect. PubMed https://doi.org/10.1038/s41598-019-49189-8, DOI: https://doi.org/10.1038/s41598-019-49189-8. Clostridium difficile is responsible for human diseases ranging from mild diarrhea to pseudomembranous colitis1. An odds ratio of one indicates that the community DNA has the same proportion of hits to a given category as the comparison data set; an odds ratio greater than one indicates enrichment (more hits to a given category than expected), whereas an odds ratio less than one indicates underrepresentation (fewer hits to a given category than expected). Additional metagenomic analysis using a shotgun approach, versus a 16S ribosomal RNA approach, indicates a diversity of gut microbiota at both the genera and gene level (Baumann-Dudenhoeffer et al., 2018; Stewart et al., 2018; Di Guglielmo et al., 2019). Nat. Infect. Deoxynivalenol exposure altered the gut microbiota composition in mice From the metagenomic sequencing, a total of 158.66 Gb of raw data from all samples was generated with each averaging 13.22 Gb (Fig. van Nood, E. et al. Article. DXP is a precursor in the biosynthesis of vitamins essential for human health, including B1 (thiamine) and B6 (pyridoxal form) (25). 8600 Rockville Pike ADS PMC legacy view 16S amplification and sequencing were performed as described elsewhere42. Jamnik J., Rehman S., Mejia S. B., et al. China In terms of the number of genus with significant differences (P value 0.05), the T group was significantly more than the H group, which was exactly matched with the patient's phenotype, that the patients of the T group had more acute onset and more obvious inflammatory response than the patients of the H group. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bacteroidetes were significantly underrepresented in the CDI group (p=0.007). Copyright 2021 Elsevier B.V. All rights reserved. The clean reads were mapped to the human gut microbiome integrated gene catalog (IGC) (J. Bifidobacterium bifidum is associated with prevention of the first episode of CDI37. Basic Medical College, Hebei University of Chinese Medicine, Shijiazhuang 050200, PR China N. Engl. Clostridium butyricum Strains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates. Sci. The https:// ensures that you are connecting to the A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection. Article Researchers of a metagenomic analysis assessed the taxonomic and functional signatures of the gut microbiome in gout and its association with clinical parameters and response to therapeutic interventions. The human distal gut microbiome is enriched for -glucosidase (COG1472, COG2723 in table S4; P < 0.0005; glycosidase families GH3 and GH9 in table S5). please go to the Copyright Clearance Center request page. At this time, it is not clear whether these differences reflect limited coverage of their microbiomes or other factors such as host diet, genotype, and life-style. The results showed a decrease in the diversity of gut microbiome in gout patients and the gene abundance and metabolomics had great differences among study groups. All the - and -diversity statistics were performed by using vegan package of R software (v3.6.1). Introduction Use the Previous and Next buttons to navigate three slides at a time, or the slide dot buttons at the end to jump three slides at a time. Compared with healthy people, the content of uric acid in the serum increases, which is largely related to the poor excretion of uric acid by the kidneys and intestines [4]. In conclusion, our results demonstrated an appreciable capability of JP to restore the gut microbiota profile altered by AOM/DSS, indicating the potential of jujube polysaccharides as promising prebiotic candidates for the prevention and treatment of colorectal cancer. Periodic sampling of the distal gut microbiome (and of our other microbial communities) may provide insights into the effects of environmental change on our microevolution. The results should provide a broader view of human biology, including new biomarkers for defining our health; new ways for optimizing our personal nutrition; new ways for predicting the bio-availability of orally administered drugs; and new ways to forecast our individual and societal predispositions to disorders such as infections with pathogens, obesity, and misdirected or maladapted host immune responses of the gut. Federal government websites often end in .gov or .mil. Culturing of unculturable human microbiota reveals novel taxa and extensive sporulation. 368, 407415 (2013). Primary fermenters process glycans to short-chain fatty acids (SCFAs), mainly acetate, propionate, and butyrate, plus gases (i.e., H2 and CO2). Dhariwal, A. et al. Correlation analysis between the medical examination index and species on the phylum level and genus level. Detoxification of xenobiotics could impact the host in a variety of ways, ranging from susceptibility to cancer to the efficiency of drug metabolism. Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies. Infect. Google Scholar. Carousel with three slides shown at a time. However, the distal gut microbiome provides us with this capacity (1) (Fig. Similar analyses based on a 99% similarity threshold are provided (11). CAS These reads represented a total of 1,617,706 bp of DNA sequence, which corresponds to ~0.7-fold coverage of the B. longum genome. Our experience in culturomics23 enabled us to select the most profitable growing conditions. Clin. Nature 486, 207214 (2012). Stool samples were analyzed with metagenomics focused on the V3-V4 of the 16S DNA gene thanks to the MiSeq technology (Illumina, San Diego, USA). Forty percent of the reads (56,292 total) could not be assembled into contigs, most likely because of a combination of low depth of coverage and low abundance of some organisms within the specimens. successfully administrated to two patients with recurrent CDI a cocktail of 33 bacteria15 selected after culture of a stool from a healthy subject in strict anaerobic conditions. Opin. selected twelve bacteria; some of them were shown to inhibit C. difficile growth in vitro. Biochemical indicators (please refer to Table S4.pdf). There have been many advances in the research on the pathogenesis of gout and the effect of drugs, no matter from the biochemical indicators, molecular mechanism, or omics including genomics, transcriptomics, epigenomics, and metabolomics. It indicated that the gut microbiota diversity of gout patients (group A vs B) was lower than the healthy control samples (group Con). we analyzed amplicon libraries and metagenomic libraries obtained for six species of higher termites to compare the structure and functional potential of the intestinal microbiota in the major gut compartments. By submitting a comment you agree to abide by our Terms and Community Guidelines. The number of bacterial genera also had significant differences among treatment groups. Download PDF View Record in . For the CDI group, we selected three stool samples: one of 027 genotype, one of 078 genotype and one of neither 027, nor 078 genotype. Trend chart of species abundance on the phylum level in three groups. Meanwhile, only 153 differential KOs were detected between A-B and only the pathway, glutathione metabolism was significantly enriched, and biosynthesis of antibiotics, carbon metabolism, metabolic pathways, photosynthesis, and pyruvate metabolism were common significantly enriched between group A vs Con and group B vs Con (Figure 3 and Figures S2D-S2E). Several COGs responsible for fucose utilization are enriched in the human gut microbiome relative to all microbial genomes (table S4). Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. Patro R., Duggal G., Love M. I., Irizarry R. A., Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Then, the reads with high quality from each sample were aligned against Integrated Gene Catalog (IGC, v100064) (J. Would you like email updates of new search results? Infect. PubMed Central Bacteroides ovatus, Bifidobacterium adolescentis, Bifidobacterium longum, have been used by Petrof et al.15. Shi G, Lin Y, Wu Y, Zhou J, Cao L, Chen J, Li Y, Tan N, Zhong S. Nutrients. From the significantly different species at the genus level between group A and group B, we found these genera mainly belonged to the Proteobacteria phylum, of which five genera were more in group A and less in group B, and they were all pathogenic bacteria, so it can be easily understood that our drugs help inhibiting the reproduction of pathogenic bacteria of these five genera and help patients to restore normal intestinal levels. Their stools were tested negative for C. difficile by RT-PCR. The culturomic approach22 allowed an increase of known gut bacteria. 2019 Dec 25;12(1):62. doi: 10.3390/nu12010062. Huttenhower, C. et al. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. The aim of this study was to investigate the modulatory effects of jujube polysaccharides (JP) on intestinal microbiota, and the influence of JP on the gut flora structure was then analyzed using an AOM/DSS-induced colitis cancer mouse model, using high-throughput sequencing. Progress made with 16S rDNA-based enumerations has disclosed significant differences in community membership between healthy adults (2, 3), differences that may contribute to variations in normal physiology between individuals or that may predispose to disease. Lee, Y. J. et al. We found that the distinction between group A and B was not large, and the distinction between group A vs Con or between group B vs Con was more obvious by comparing group A and B and Con (Figure 1(b)), indicating that the gut microbiota of gout patients and nongout patients were different, but the effect on the gut microbiota between medication before and after was not significant. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. (3) Figure S3. Further explorations are needed before probiotic utilization. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. If, despite the good spectra quality, the bacteria has not been identified, a 16S rDNA gene sequencing of the bacteria has been performed. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Metagenomics is the gold standard method to study gut microbiota19,20, but a large part of the detected bacteria has never been cultivated21. Microbiota composition was different for the two groups. The number of KEGG pathways and COG terms enriched in the human distal gut microbiomes of subjects 7 and 8 is listed in table S2. The objective was to explore the dynamic changes of gut microbiota in healthy centenarians and centenarians approaching end of life and to unravel . Google Scholar. The authors thank culturomic students for their work. Among the 35 bacteria detected by metagenomics and associated with a healthy microbiota, 26 have been identified up to the species level and are currently cultivable (Fig. However, we found that previous studies on the gut microbes of patients with gout, whether using16S rRNA or metagenomics, were limited to the difference in the composition and abundance of the species between gout patients and healthy controls, little using groups of patients before and after medication to study the changes in gut microbes. 2A). Among these 14 bacteria, 9 (64.3%) belonged to the phylum Bacteroidetes, 3 (21.4%) to the phylum Firmicutes, 9 (64.3%) had already been cultivated from the human gut and 5 (35.7%) had been discovered by previous culturomic studies. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Therefore, superorganismal view of our genetic landscape should include genes embedded in our human genome and the genes in our affiliated microbiome, whereas a comprehensive view of our metabolome would encompass the metabolic networks based in our microbial communities. Schubert, A. M. et al. HHS Vulnerability Disclosure, Help Not only bacteria but also environment and interactive molecules produced by them are effective for restoration of gut homeostasis39. (2017). Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. The human genome lacks most of the enzymes required for degrading these glycans (20). Then, we generated the species, KO, and pathway abundance profiles by the gene abundance profile and then performed the different analysis between groups. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Anderson KM, Ferranti EP, Alagha EC, Mykityshyn E, French CE, Reilly CM. These families are associated with resistance against C. difficile30,31,32,33. (10) have demonstrated the utility of this approach for studying mixed microbial communities. HHS Vulnerability Disclosure, Help In the control group, we obtained 275 different species with a mean of 86 bacteria per sample. All enzymes necessary to convert DXP to IPP and thiamine are enriched (P < 0.0001 relative to all sequenced microbes). COG analysis reveals metabolic functions that are enriched or underrepresented in the human distal gut microbiome (relative to all sequenced microbes). Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology. Thank you for visiting nature.com. Lagier, J.-C., Dubourg, G., Amrane, S. & Raoult, D. Koch Postulate: Why Should we Grow Bacteria? A total of 50,164 open reading frames (ORFs) were predicted from the data set (25,077 for subject 7 and 25,087 for subject 8). Compared to 16S analysis, metagenomics analysis could find that the intestinal microbiota of gout patients was highly distinct from healthy individuals in both organismal and functional structures, even build up a diagnosis model as a possible future application approach, higher than the blood-uric-acid based approach [ 22 ]. (ad) The group comparisons of a&b&con, a&b, a&con, and b&con, respectively. Clin. DOI: 10.5713/ajas.15.0026 Corpus ID: 18513810; Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens A Review @article{Choi2015MetagenomicAO, title={Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens A Review}, author={Ki Young Choi and Tae Kwon Lee and Woo Jun Sul}, journal={Asian-Australasian Journal .
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