To detect any differences in gut bacterial diversity between the two groups, alpha diversity indexes (Shannon and Simpson) and a beta diversity index (BrayCurtis distance) were computed. H-MX was partially supported by the National Key R&D Program of China (2016YFC1201805 and 2017YFC1001100). It integrates ORF finder, Pfam domain detection software and statistical analysis tools to a user-friendly web interface for functional comparison of metagenomic data from multiple samples [101]. The CDS of all samples were clustered by CD-HIT v4.6.1 to obtain unigenes. According to our metagenome sequencing results, Cephamycin C biosynthesis genes were encoded by the s__Clostridiales_bacterium, s__Paenibacillus_chitinolyticus, s__Paenibacillus_sp._G4, and so on. Agrawal S., Agrawal A., Said H. M. (2016). Metagenomic analysis of the human distal gut microbiome. Index values j express the similarity of the sets of most central nodes and also of the sets of hub taxa between the two networks. The gut microbial community structure and function have been studied in different host species, including mouse [12], human [13], canine, [14], feline [14], cow [15], and yak [15]. In fact, studies with discrete population groups have indicated that the super-kingdom level conservation rapidly disappears lower in the phylogenetic hierarchy, giving rise to a microbiota fingerprint of an individual at the levels of genus, species, and strain. Our results indicated that CMC could improve the gut bacterias biotin synthesis and thus should be good for host health. Although we have determined the correlations between GM and CMC, further studies are still needed to elucidate its mechanisms; (3) This study does not allow for controlling all potential confounding factors that might have effect on human gut microbiome, which may lead to some statistical artifacts; (4) In this study, we used an American cohort as the validation cohort. This study further supports the biological value of . Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-. The increase of the bacteria g_Anaerostipes in the CMC group may also contribute to intestinal health. ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz. Received 2014 Jul 8; Revised 2015 Feb 10; Accepted 2015 Feb 26. This site needs JavaScript to work properly. According to the metagenome analysis, our results indicated that the gut microbiota in PTB patients was significantly different from healthy control samples as characterized by the bacteria and metabolic pathway. Most of the aforementioned tools use known 16S rRNA reference sequence databases like RDP (http://rdp.cme.msu.edu/) and Greengenes (http://greengenes.lbl.gov) to assign taxonomy information to the unknown sequence. Mounier J., Monnet C., Vallaeys T., Arditi R., Sarthou A.S., Helias A. Microbial interactions within a cheese microbial community. Starting with the first-generation Sanger (e.g., Applied Biosystems) platforms to the second-generation 454 Life Sciences Roche (e.g., GS FLX Titanium) and Illumina (e.g., GA II, MiSeq, and HiSeq) platforms and finally, the recently developed Ion Torrent Personal Genome Machines (PGM) and Single-Molecule Real-Time (SMRT) third generation sequencing techniques introduced by Pacific Bioscience have evolved according to the need for generating cost-effective and faster metagenomic sequencing techniques. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. The similarity-based network inferences are based on co-occurrence and/or mutual exclusion pattern of two species over different sampling conditions. Emerging evidence has indicated an association between the gut microbiome and arthritis diseases including gout. -. The role of milk components, Pro-, Pre-, and synbiotic foods in calcium absorption and bone health maintenance. JS was partially supported by grants from the Science and Technology Program of Guangzhou, China (201604020007), and the National Natural Science Foundation of China (81770878). Epub 2016 Jun 7. CD-HIT-OTU is a clustering program able to process millions of rRNAs in a few minutes. Our latest research showed that BDB could alleviate T2DM in diabetic BKS db mice. There are many standalone tools, which may be used for the analysis of 16S rRNA marker gene sequencing data and the WGS data. Although the role of viral species in human diseases is far from fully appreciated, inter-kingdom interactions between bacteria, viruses, and eukaryotes in the intestine have been shown to influence virulence of the organisms and pathogenesis [59]. Cuevas-Sierra A., Ramos-Lopez O., Riezu-Boj J. I., Milagro F. I., Martinez J. cow milk consumption; functional module; gut microbiota; metagenomic; network. sharing sensitive information, make sure youre on a federal Genomics Proteomics Bioinformatics. Green edges correspond to positive estimated associations and red edges to negative ones. Establishing a model of the gut microbial interaction network is a major challenge for the scientific community and little progress has been made in this area. Clipboard, Search History, and several other advanced features are temporarily unavailable. 2012; Turnbaugh et al. Diversity in the fecal bacterial and fungal communities was also reflected in studies on canine and feline gut samples [25]. It enables the user to annotate multiple metagenomes at a time and also to compare the metabolic data [103]. Typically, human gut microbiota behaves like a multicellular organ, which consists of nearly 200 prevalent bacterial species and approximately 1000 uncommon species [1]. Specifically, taxa g_Anaerostipes (p < 0.01), g_Bacteroides (p < 0.05), s_Anaerostipes_hadrus (p < 0.01), and s_Bifidobacterium_pseudocatenulatum (p < 0.01) were positively correlated with CMC levels, but p_Actinobacteria (p < 0.01) and g_Bifidobacterium (p < 0.01) were negatively associated with CMC levels. The https:// ensures that you are connecting to the Online ahead of print. Bacterial species that were reported with increased abundance under certain disease conditions are mentioned in Table 2. Bethesda, MD 20894, Web Policies We observed different hub taxa in the CMC group compared with the control group, which indicated that CMC may at least partially change the interaction of GM. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on. Please enable it to take advantage of the complete set of features! We selected the best hit with the highest bit score from all the potential hits (E-values 1 105) as the respective KEGG Orthology (KO) for each unigene. Ley R. E., Hamady M., Lozupone C., Turnbaugh P. J., Ramey R. R., Bircher J. S., et al. will also be available for a limited time. MAG abundance data and sample data were processed by the phyloseq function in the phyloseq package in R. We selected the 100 taxa with the highest abundance to calculate their association in the gut. For the TSS transformed data analysis, RA of one phylum (p_Actinobacteria), three genera (g__Bifidobacterium, g__Anaerostipes, g__Bacteroides), and 28 species were altered in the CMC group versus the control group (P < 0.05) and only two (g__Bacteroides, PCLR = 0.084; s__Prevotella_copri_CAG_164, PCLR = 0.057) of these taxa have not been observed to diversify significantly in the CLR transformed data analysis. Front Immunol. Using 16S rRNA sequencing, common microbes that belong to the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum had been identified in the intestines of mice, rats, and humans [24]. Commensal microbiota of the intestine play a key role in normal anatomical development and physiological function of the human intestine as well as other organs or systems, such as the brain [27] and the metabolic [28] and immune systems [29]. X66 had the highest degree of 23, highest closeness centrality of 0.836, and highest eigenvector centrality of 1.000. Bendtsen L. Q., Bldel T., Holm J. The ePub format is best viewed in the iBooks reader. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. In contrast, WGS additionally explores the functions of the metagenome. P (J j) is the probability that Jaccards index takes a value less than or equal to the calculated index j for the present total number of taxa in both sets and P (J j) is defined analogously. This is an important pathway involved in the biosynthesis of SCFAs butyrate (Portincasa et al., 2022). (2020). Am. Alpha diversity of subjects grouped by CMC status. Several efforts have been previously made in this regard. Functional metagenomics may be useful, but currently the objective of sequencing is to identify functionally-important non-abundant genes. We collected stool samples from all subjects. Another study has shown that g_Bacteroides can activate T cells in the bodies of infants, thereby promoting their immune system development (Walker and Iyengar, 2015). Careers. Data were normalized via total sum scaling (TTS) method and are expressed as relative abundance. There were 4 significant differences (p < 0.05) in the two groups which belonged to four metabolic categories, including endocytosis, phosphotransferase system (PTS), toluene degradation, and amoebiasis. The pilot study . However, this type of approach cannot be applied to complex, nonlinear, and evolving systems, where more than one dominant species are present at any point of time and the abundance changes over time. 3-bromo-4,5-bis (2,3-dibromo-4,5-dihydroxybenzyl)-1,2-benzenediol (BDB) is a natural bromophenol isolated from marine red alga Rhodomela confervoides. Modularity of MG-RASTallows new analysis steps or comparative data to be added during the analysis according to the users need. The data were normalized by the total sum scaling method. The human gut is populated by trillions of microorganisms, known collectively as the gut microbiota (GM) (Ley et al., 2008). Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn's disease (CD), two major forms of inflammatory bowel diseases (IBD). Large numbers of metagenomic sequence datasets have been generated, thanks to the advances in WGS and 16S rRNA pyrosequencing techniques [17]. 2015;230:165180. METAREP: JCVI metagenomics reportsan open source tool for high-performance comparative metagenomics. The present study provided a detailed analysis of the characterization of the gut microbiota in patients based on the clinic. (A) Microbial genes annotated, MeSH Learn more It could also ameliorate gut flora dysbiosis, especially the depletion of the SCFA-producing bacteria Anaerostipes (Muoz-Tamayo et al., 2011). Mason M. R., Preshaw P. M., Nagaraja H. N., Dabdoub S. M., Rahman A., Kumar P. S. (2015). Eigenvector centrality is used for defining hubs (nodes with a centrality value above the empirical 95% quantile) and scaling node sizes. 8600 Rockville Pike Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Data were normalized via total sum, Bacterial associations of samples in two groups. Disclaimer, National Library of Medicine For beta diversity, at the phylum level, no significant difference was observed (PPCoA < 0.22 and PNMDS < 0.223) (Figure 2A and Supplementary Table 2); at the genus level, significant p-values were achieved (PPCoA < 0.039 and PNMDS < 0.037) (Figure 2B and Supplementary Table 2); as for the species level, two nearly significant p-values were observed (PPCoA < 0.055 and PNMDS < 0.055) (Figure 2C and Supplementary Table 2). Wolvers D., Antoine J.M., Myllyluoma E., Schrezenmeir J., Szajewska H., Rijkers G.T. Milk and dairy products are frequently included as important elements in a healthy and balanced diet, which can provide the necessary energy and nutrients to ensure proper growth and development (Pereira, 2014). Accessibility official website and that any information you provide is encrypted Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. WGS is also useful for a detailed understanding of the functional potential of the microbiome. . In such cases, the regression model and rule-based model are used, where the abundance of one species is predicted from combined abundances of the organisms in the system [76]. Zhang C., Zhang M., Wang S., Han R., Cao Y., Hua W. Interactions between gut microbiota host genetics and diet relevant to development of metabolic syndromes in mice. Xiao S, Zhang G, Jiang C, Liu X, Wang X, Li Y, Cheng M, Lv H, Xian F, Guo X, Tan Y. The richness of the gut microbiota in patients was revealed. Balamurugan R., Rajendiran E., George S., Samuel G.V., Ramakrishna B.S. Clipboard, Search History, and several other advanced features are temporarily unavailable. Introducing mothur: open-source platform-independent community-supported software for describing and comparing microbial communities.
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