Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD. Badri M., Kurtz Z. D., Bonneau R., Mller C. L. (2020). CLR data norm method was used and the association was calculated using the SPRING method (Yoon et al., 2019). 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]. In their study, they conducted metagenomics, metatranscriptomics, and metaproteomics on stool and serum samples from 132 subjects for 1 year. Asquith M., Elewaut D., Lin P., Rosenbaum J.T. COG analysis reveals metabolic functions that are enriched or underrepresented in the human distal gut microbiome (relative to all sequenced microbes). 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. All procedures followed the tenets of the Declaration of Helsinki and were approved by the Ethics Committee of Chongqing Medical University with written informed consent. Despite inter-species differences in community structure and function, gut microbiota frequently play a beneficial role in host metabolism and immunity across different species [16]. FOIA In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. It was hypothesized that the above-mentioned changes of the gut microbiota could exert an impact on the development of PTB through the downstream regulation of the immune status of the host by way of the gut-lung axis. and Bacteroides spp., whereas healthy controls have higher abundance of . Gerlach W., Junemann S., Tille F., Goesmann A., Stoye J. WebCARMA:a web application for the functional and taxonomic classification of unassembled metagenomic reads. 8600 Rockville Pike Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, Hou S, He Y, Xu Q, Xiong X, Kijlstra A, Qin N, Yang P. Microbiome. World J Gastroenterol. A systems biology approach may be required with a therapeutic goal to restore the biochemical, proteomic, and metagenomic profiles of an individual. Th17 cells in primary Sjgren's syndrome negatively correlate with increased. Kelder T., Stroeve J.H., Bijlsma S., Radonjic M., Roeselers G. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health. Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S. 2 We further studied the GM association network in each group via the NetCoMi package to better understand the complex interplay of microbial communities. Microbiota has great potential for the identification of genetic biomarkers of disease, but proper statistical analysis is extremely difficult. Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type. Therapeutically active metabolite 5-aminosalicylate is released from the prodrug sulfasalazine, while digoxin may be converted to less active reduced derivatives by the action of colonic microflora [34,67]. LEfSe indicates differences in the bacterial taxa at different, Differences of taxa abundance present in subjects. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. For the network comparison, the 50 most abundant taxa were chosen. After being filtered by the criteria RA > 0.01%, the total number of phyla was 59 in both groups, but the total number of genera and the total number of species was slightly lower in the CMC group: There were 2,097 genera and 3,426 species in the control group, whereas there were 2,090 genera and 3,354 species in the CMC group (Table 2). Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic . Aerobic exercise can increase g_Bacteroides abundance and thus improve cardiopulmonary function (Morita et al., 2019). However, a single pathobiont (commensal turned into a pathogen) has also been reported to cause disease under specific genetic and environmental conditions. PubMed publications on different diseases involving gut microbiota were searched on February 09, 2015. Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis. For further community composition analysis, the data were filtered by several criteria: (1) relative abundance > 0.1%; (2) detection rate within all samples > 10%; and (3) low variance filter for comparative analysis: inter-quantile range (IQR) > 10%. CLR transformation could theoretically avoid the compositional effects of microbiome data (McMurdie and Holmes, 2014). Lingner T., Asshauer K.P., Schreiber F., Meinicke P. CoMeta web server for comparative functional profiling of metagenomes. 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. showed that genomic variations within species altered their phenotype and environmental adaptation [81]. Garmendia L., Hernandez A., Sanchez M.B., Martinez J.L. While the manipulation of microbiota has immense therapeutic potential, techniques need to be developed to manipulate individual bacteria within a community and for targeted therapy, such as designer probiotics. It also provides Gene Ontology (GO), NCBI Taxonomy and KEGG Pathway Browser-based comparison of multiple datasets at various functional and taxonomic levels [98]. Further studies of them, especially those focused on their interplay with other microbes, should be helpful for elucidating CMCs effects on GM. Dysbiotic events in gut microbiota: impact on human health. Alam M.Z., Alam Q., Kamal M.A., Abuzenadah A.M., Haque A. A total of 214 species belonging to 52 genera and 7 phyla remained after the data processing. Our research aims to investigate the changes in human gut microbial composition in Chinese peri-/postmenopausal women with different CMC habits. . The fecal samples were frozen at -80C within 30 min of sample procurement and used for GM DNA extraction with the E.Z.N.A. Stool DNA Kit (Omega, Norcross, GA, United States). The inhibition of cephamycin C biosynthesis may also be beneficial to gut probiotics, as it is a kind of antibiotic and may affect the balance of intestinal flora. -, Brooke JS. sharing sensitive information, make sure youre on a federal XC was partially supported by the Research Foundation of the Ministry of Education of China (8091B022138). a The heatmap of 25 tracer genes abundance for each MGS, Effect of transplantation of feces from BD patients on EAU. This is consistent with a report showing that an increase of g_Bacteroides usually results from the long-term intake of protein and animal fat (Wu et al., 2011). Second, as shown in Table 6, the degree, betweenness centrality, closeness centrality, and eigenvector centrality of certain nodes were different across groups. METAGENassist, a web server for comparative metagenomics, can be used for comprehensive multivariate statistical analyses on the bacterial census data from different environment sites or different biological hosts selected by the users [100]; CoMet, another web-based comparative metagenomics platform is used for the analysis of metagenomic short read data resulting from WGS-based studies. Mounier J., Monnet C., Vallaeys T., Arditi R., Sarthou A.S., Helias A. Microbial interactions within a cheese microbial community. A primer on metagenomics. 2016 Aug;169:28-35. doi: 10.1016/j.clim.2016.06.002. HiFi. doi: 10.1007/978-3-319-18144-8_8. These datasets are available in different repositories including the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra), the Data Analysis and Coordination Center (DACC) under the Human Microbiome Project (HMP) (http://hmpdacc.org) supported by the National Institutes of Health (NIH), metagenomic data resource from the European Bioinformatics Institute (EBI) (https://www.ebi.ac.uk/metagenomics/) and the UniProt Metagenomic and Environmental Sequences (UniMES) database (http://www.uniprot.org/help/unimes). Mauricio M. D., Serna E., Fernndez-Murga M. L., Portero J., Aldasoro M., Valles S. L., et al. LDA, LDA score of LEfSe analysis of American cohort. Z., Abe F., Benno Y. An official website of the United States government. Metagenomic analysis of gut microbiota modulatory effects of jujube (Ziziphus jujuba Mill.) Data were normalized via total sum scaling (TTS) method and are expressed as relative abundance. CMC alters the functional potential of the gut microbiome. Pooled feces from healthy individuals and PBS were transferred to mice as control groups. Gut microbiota complements the biology of an organism in ways that are mutually beneficial [5]. Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Falchi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Cow milk consumption (CMC) and alterations of gut bacterial composition are proposed to be closely related to human health and disease. The .gov means its official. 2021 Apr 1;11:605825. doi: 10.3389/fcimb.2021.605825. These taxa were the same as those most significant ones in the MannWhitney test. There is still limited knowledge about the gut microbial interactions and interactions between the microbes and the host. Waste not, want not: why rarefying microbiome data is inadmissible. It plays a key role in the function of natural killer (NK) lymphocytes and the generation of cytotoxic T lymphocytes (Kuroishi, 2015; Agrawal et al., 2016). Published by Elsevier Masson SAS.. All rights reserved. However, not much is known about the regulation of BAs during progression to type 1 diabetes (T1D). (3) Read alignment to the host genome was performed by Bowtie2 v2.2.0 and host genomic contamination was removed. Each subject completed a questionnaire that collected their CMC status and other basic information like age, weight, medication, alcohol drinking, diet, smoking history, and use of nutrition supplements. According to the LEfSe results, a total of 36 taxa correlated with CMC (p < 0.05, | LDA| > 2.0), but only five of these taxa reached FDR < 0.1. They are s__Ruminococcus_gnavus (X117), s__Faecalibacterium_prausnitzii (X9), s__Prevotella_copri (X158), s__Clostridium_sp._CAG.7 (X44), s__Roseburia_sp._CAG.18 (X138), s__Prevotella_sp._CAG.386 (X530), and s__Bacteroides_dorei (X14). The gut microbiota is crucial in the regulation of bile acid (BA) metabolism. Gut ecosystems are currently being studied in the native state using 16S rRNA gene amplicon sequencing or whole genome sequencing (WGS) techniques [11]. 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. ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz, https://www.frontiersin.org/articles/10.3389/fmicb.2022.957885/full#supplementary-material, https://www.ncbi.nlm.nih.gov/books/NBK547751/. It is recognized that microbial dysregulation contributes to the pathogenesis of tuberculosis (TB) but the underlying mechanisms remain unclear. The tool MEtaGenome ANalyzer (MEGAN) uses BLAST search against a reference sequence database like non-redundant sequence database from NCBI NR database and provides results in a graphical user interface (GUI). Here, 16S rRNA marker genes were used for compromised gut in children with anti-islet cell autoimmunity [75]. (2021). Bioinform 2:lqaa100. Metagenome-Assembled Genome (MAG) counts at the phylum, genus, and species levels in each group were calculated within R by the criteria that one feature is taken into account only if its RA is more than 0.01% after TSS data transformation. 2022 Oct 5;13:974648. doi: 10.3389/fimmu.2022.974648. Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice. Smoking and colorectal cancer: a meta-analysis. Species represented by the nodes are given in Supplementary Table 5. Microbial networks in SPRING - semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data. The immune homeostasis of the host is also influenced by gut microbiota (Mason et al., 2015). Some studies also show an advantage of s_B.pseudocatenulatum in treating obesity-associated diseases (Mauricio et al., 2017; Sanchis-Chord et al., 2019). It was indicated that CMC may influence the proportional composition of gut microbiota which utilize different PTS-related enzymes. Emerging evidence has indicated an association between the gut microbiome and arthritis diseases including gout. The ligated products were amplified with polymerase chain reaction (PCR) under the following conditions: initial denaturation at 95C for 3 min, followed by 8 cycles of 98C for 15 s (denaturation), 60C for 15 s, 72C for 30 s (extension), and then a final elongation at 72C for 5 min. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Hemarajata P., Versalovic J. Bookshelf Just same as that in the Chinese cohort, the data were normalized via TSS or CLR and LEfSe was used to detect the differential microbiota across groups in the American cohort. KEGG module analysis revealed 48 gut microbiome functional modules significantly (p < 0.05) associated with CMC, including Vibrio cholerae pathogenicity signature, cholera toxins (p = 9.52e-04), and cephamycin C biosynthesis module (p = 0.0057), among others. Several factors, such as diet and genetic background of the host and immune status, affect the composition of the microbiota [2,3]. 2015;230:165180. For this study, LEfSe was performed given two indispensable situations: (1) threshold on the logarithmic LDA score for discriminative features was equivalent to 2.0; and (2) p-value < 0.05 and FDR-adjusted p < 0.1. government site. Relative abundance (RA) of one phylum (p_Actinobacteria), three genera (g_Bifidobacterium, g_Anaerostipes, and g_Bacteroides), and 28 species diversified significantly across groups. For the functional module analysis, MannWhitney test was applied to assess the richness differences. METAREP: JCVI metagenomics reportsan open source tool for high-performance comparative metagenomics. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Clipboard, Search History, and several other advanced features are temporarily unavailable. The sum of RA of unigenes within a module represented the RA of an annotated functional module. Background: Perfluorooctane sulfonate (PFOS) is a persistent environmental pollutant that has become a significant concern around the world. These uncultured genomes substantially. 2015 Jun; 13(3): 148158. However, the results are less-encouraging in obesity and chronic diseases like diabetes mellitus, IBD, and IBS [53]. -, Badri M., Kurtz Z. D., Bonneau R., Mller C. L. (2020). Biotin regulates immunological and inflammatory functions. HHS Vulnerability Disclosure, Help This further suggests that every individual carries a unique metagenome, which can be exploited further for personalized medicine or dietary modifications [80]. Of these, 38 significant modules increased in the CMC group, including dissimilatory sulfate reduction (p = 0.0016); PTS system, lactose-specific II component (p = 0.0021); PTS system, fructose-specific II component (p = 0.0035); pimeloyl-ACP biosynthesis (p = 0.005), and others. Another online tool, CD-HIT, can be used in identification of non-redundant sequences and gene-families by clustering raw reads [99]. 2020 May 3;11(3):539-555. doi: 10.1080/19490976.2019.1700754. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbemicrobe interaction networks. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. The cow milk was pasteurized. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E. Clin Immunol. Biotin deficiency enhances the inflammatory response of human dendritic cells. Goll J., Rusch D.B., Tanenbaum D.M., Thiagarajan M., Li K., Methe B.A. Design The gut microbiota of 270 overweight/obese women participating in a mother-infant clinical study were analysed with metagenomics approach in early (mean gestational weeks 13.9) and late (gestational weeks 35.2) pregnancy. 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. The .gov means its official. Results recently built a gut microbiota network with co-occurrence relationship using Spearman rank correlation method. Linear discriminant analysis effect size (LEfSe) analysis was conducted to identify the correlation between gut microbiota and CMC. Diversity in the fecal bacterial and fungal communities was also reflected in studies on canine and feline gut samples [25]. Data were normalized via the TSS method. Current therapies are limited to non-specifically targeting the microbiota with probiotics, prebiotics, and synbiotics to restore the healthy flora [7073]. 311 C386C391. Modularity of MG-RASTallows new analysis steps or comparative data to be added during the analysis according to the users need. Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X. There are many standalone tools, which may be used for the analysis of 16S rRNA marker gene sequencing data and the WGS data. HX: methodology. ObjectivesGut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. It determines the bit score and expected value (E-value) of the computed alignment, which indicates the alignment quality. (2021). Study record managers: . Breast cancer in postmenopausal women is associated with an altered gut metagenome. Comparative analysis of metagenomics abundance data integrated with databases like KEGG Orthology, COG, PFAM and TIGRFAM, Classification short metagenomic reads (75100bp) into specific taxonomic, Phylogenetic classification of metagenomic short reads using interpolated Markov models, Fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades, Correlation of tetranucleotide usage patterns in DNA, Flexible comparative metagenomics framework, Performs comprehensive multivariate statistical analyses on the data from different host and environment sites, ORF finding and subsequent Pfam domain assignment to protein sequences, Unassembled reads as short as 35bp can be used for the taxonomic classification with less false positive prediction, High-throughput pipeline for functional metagenomic analysis, Provides list of workflows for WGS data analysis, Implemented to run in parallel on local computer cluster. Teeling H., Waldmann J., Lombardot T., Bauer M., Glockner F.O. Animal Model Exp Med. 2022 Jul 19;12(7):1742. doi: 10.3390/diagnostics12071742. -. (2016). [4][5] Minimum number of edges or vertices (nodes) that need to be removed to disconnect the network, respectively. A core gut microbiome in obese and lean twins. The study found large differences in the gut flora between the two groups which suggested an invasion of the gut . We thank the National Institutes of Health for financial support and LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China, www.lc-bio.com) for technical support for our research. Jie Z., Liang S., Ding Q., Li F., Sun X., Lin Y., et al. Of note, in the Chinese cohort, both p_Actinobacteria and g_Bifidobacterium were detected to be negatively associated with CMC (FDR < 0.1 and LDA < 2). Among them, RA of p_Actinobacteria (FDR = 0.0049, LDA score = 2.19), g_Bifidobacterium (FDR = 0.019, LDA score = 2.19), and s_Bifidobacterium_unclassified (FDR = 0.093, LDA score = 3) decreased in the CMC group, but RA of g_Anaerostipes (FDR = 0.019, LDA score = 3.21) and s_Anaerostipes_hadrus (FDR = 0.093, LDA score = 3.21) increased. Copyright 2022 Tian, Yao, Lin, Lv, Jiang, Wang, Shen, Xiao, Xu, Xu, Cheng, Shen, Qiu, Luo, Zhao, Yan, Deng and Zhang. Li.s conclusion that whole milk consumption significantly increased Anaerostipes (p < 0.01) (Li et al., 2018). The 100 most abundant taxa were analyzed in this part and (A) the complete association network where the 50 nodes with the highest degree are shown. The gut is an important target organ for stress after sepsis, trauma, burn, and shock [ 14 ]. The distal gut is home to our largest number of microbes. Generating an ePub file may take a long time, please be patient. A cohort of 517 unrelated healthy Chinese peri-/postmenopausal women were recruited from June 2014 to January 2018 from local communities. Before Morowitz M.J., Denef V.J., Costello E.K., Thomas B.C., Poroyko V., Relman D.A. Research progress on the relationship between intestinal microecology and intestinal bowel disease. 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).
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