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]. PMC 10.1152/ajpcell.00141.2016 Our research aims to investigate the changes in human gut microbial composition in Chinese peri-/postmenopausal women with different CMC habits. sequenced the viromes isolated from fecal samples of monozygotic twins and their mothers, and compared them with the total fecal DNA. Companion animals symposium: microbes and gastrointestinal health of dogs and cats. Disease, Sequencing, 16S rRNA, Operational taxonomic unit, Microbial interaction network. [4][5] Minimum number of edges or vertices (nodes) that need to be removed to disconnect the network, respectively. . Mauricio M. D., Serna E., Fernndez-Murga M. L., Portero J., Aldasoro M., Valles S. L., et al. Flint H.J., Bayer E.A., Rincon M.T., Lamed R., White B.A. Microbial networks in SPRING - semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data. Microbiota has great potential for the identification of genetic biomarkers of disease, but proper statistical analysis is extremely difficult. However, a major challenge in the study of gut microbiota is the inability to culture most of the gut microbial species [10]. These adapters also contained sequencing primer hybridization sites for single, paired-end, and indexed reads. In ruminants, the common rumen microbes are Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, Butyrivibrio fibrisolvens, and Prevotella In addition, metaphor package is also available for users having expertise in R statistical language (http://CRAN.R-project.org/package=metafor). Zhou H, Zhao X, Sun L, Liu Y, Lv Y, Gang X, Wang G. Dis Markers. All these sequence archives also provide different tools for the analysis of metagenomic sequences. Botteri E., Iodice S., Bagnardi V., Raimondi S., Lowenfels A. Gut microbiota can be modulated positively or negatively by different lifestyle and dietary factors (Gilbert et al., 2018). Ylmaz , Dolar M. E., zpnar H. (2019). Faust et al. 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. 10.1093/jn/nxab252 Kennedy P.J., Cryan J.F., Dinan T.G., Clarke G. Irritable bowel syndrome: a microbiome-gut-brain axis disorder? 10.3945/ajcn.117.158816 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). The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia. Fernndez-Murga M. L., Olivares M., Sanz Y. Gut microbiota studies in different species using pyrosequencing technology, Highly-abundant bacterial species under different disease conditions. reported that a functional core microbiome exists in human gut [4], since gut microbiota serves critical metabolic and immunological functions to maintain homeostasis. XL, H-MX, QY, and XC: conceptualization. Conclusions: Our data provide insight into the integrated responses of the host transcriptome and microbiome to dietary substrates in the early neonatal period. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. This site needs JavaScript to work properly. CD-HIT-OTU is a clustering program able to process millions of rRNAs in a few minutes. It can regulate the release of insulin and glucagon and provide energy for host cells (Hague et al., 1997). 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. In conclusion, CMC was associated with changes in gut microbiome patterns including beta diversity and richness of some gut microbiota. 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). Whereas the MiSeq platform from Illumina produces consistently higher sequence coverage in both depth and breadth, the Ion Torrent is unique for its speed of sequencing. Hub taxa usually act as connector nodes linking multiple clusters/modules in the network, thus their tiny abundance changes may affect the balance of microbe clusters apparently. Handb Exp Pharmacol. Centrality and clustering measures are adopted from the complete network. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. pseudocatenulatum. The gut microbiota shapes intestinal immune responses during health and disease. TSS is a traditional approach and has been frequently applied in microbiome analysis; however, it is strongly influenced by highly abundant taxa (Badri et al., 2020). Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents. Cuevas-Sierra A., Ramos-Lopez O., Riezu-Boj J. I., Milagro F. I., Martinez J. Current understanding of the human microbiome. powmic: an R package for power assessment in microbiome case-control studies. Shrinkage improves estimation of microbial associations under different normalization methods. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic . Aura A.M., Mattila I., Hyotylainen T., Gopalacharyulu P., Bounsaythip C., Oresic M. Drug metabolome of the simvastatin formed by human intestinal microbiota in vitro. 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]. Gerlach W., Junemann S., Tille F., Goesmann A., Stoye J. WebCARMA:a web application for the functional and taxonomic classification of unassembled metagenomic reads. 2021 Apr 1;11:605825. doi: 10.3389/fcimb.2021.605825. The richness of the gut microbiota in patients was revealed. Gut microbiota of higher vertebrates is host-specific. Greenhill C. Gut microbiota: anti-cancer therapies affected by gut microbiota. Faith J.J., McNulty N.P., Rey F.E., Gordon J.I. The relative abundance (RA) of unigenes for each sample was estimated by transcripts per kilobase million (TPM, Formula 1, where k was the kth unigene, r was the number of unigene reads, and L indicated unigene length) based on the number of aligned reads and the unigene length by Bowtie2 v2.2.0. Difference achieved significance of #P < 0.1, *P < 0.05, or **P < 0.01. Host-bacterial mutualism in the human intestine. Sichuan Da Xue Xue Bao Yi Xue Ban. Bioinform 2:lqaa100. Interestingly, the individual gut microbiota is more unique under healthy conditions than during disease, when the diversity generally decreases. Biomarkers identified by LEfSe. Second, as shown in Table 6, the degree, betweenness centrality, closeness centrality, and eigenvector centrality of certain nodes were different across groups. Odamaki T., Kato K., Sugahara H., Xiao J. BMC Pediatr. IBD, inflammatory bowel disease; T2D, type 2 diabetes; CD, Crohns disease. However, a single pathobiont (commensal turned into a pathogen) has also been reported to cause disease under specific genetic and environmental conditions. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. A systems biology approach may be required with a therapeutic goal to restore the biochemical, proteomic, and metagenomic profiles of an individual. Conclusion: Diet, gut microbiota, and obesity: links with host genetics and epigenetics and potential applications. B., Kiilerich P., et al. Data were normalized via total sum scaling (TTS) method and are expressed as relative abundance. Arndt D., Xia J., Liu Y., Zhou Y., Guo A.C., Cruz J.A. In the current study, we figured that the two groups had different beta diversity at levels of genus and species, while no difference in alpha diversity between groups was found. HX: methodology. Data were normalized via the TSS method, PERMANOVA (Permutational ANOVA) test was applied to detect the difference significance in the two groups and #P < 0.1 or *P < 0.05. We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that . PubMed publications on different diseases involving gut microbiota were searched on February 09, 2015. The datasets presented in this study can be found in online repositories. Li.s conclusion that whole milk consumption significantly increased Anaerostipes (p < 0.01) (Li et al., 2018). The present study has revealed alterations in gut bacterial composition and functional modules associated with CMC. Linear discriminant analysis effect size (LEfSe) analysis was conducted to identify the correlation between gut microbiota and CMC. Findings on the Relationship Between Intestinal Microbiome and Vasculitis. For alpha diversity, no significant difference was observed across the groups at the phylum, genus, or species levels (P > 0.05) (Figure 1 and Supplementary Table 2). We also observed alterations in the richness of PTS-related modules. Our results indicated that CMC could improve the gut bacterias biotin synthesis and thus should be good for host health. There is an urgent need for novel approaches toward the construction of gut ecosystem-wide association networks to develop global models of gut ecosystem dynamics. But the installation of QIIME needs some expertise in Linux and Windows systems, and it lacks parallel processing at the OTU picking step [82]. Clipboard, Search History, and several other advanced features are temporarily unavailable. An official website of the United States government. 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). Rodrguez-Fernndez CA, Iglesias MB, de Domingo B, Conde-Prez K, Vallejo JA, Rodrguez-Martnez L, Gonzlez-Barcia M, Lloren V, Mondelo-Garcia C, Poza M, Fernndez-Ferreiro A. Int J Mol Sci. Although these programs are widely used for metagenomic data analysis, there is still a bottleneck to identify novel bacteria, as a majority of them are unknown. Dairy consumption and physical fitness tests associated with fecal microbiome in a Chinese cohort. (2020) showed that subjects with reduced calcium consumption had a higher abundance of g_Bifidobacterium. Metagenomics coupled with bioinformatics may spearhead the bugs to drugs research. 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]. Hemarajata P., Versalovic J. The dominant species at a specific body site emerged as a hub in the network and was found to act as the signature taxa, which was responsible for the composition of each microcommunity. However, the results are less-encouraging in obesity and chronic diseases like diabetes mellitus, IBD, and IBS [53]. Current therapies are limited to non-specifically targeting the microbiota with probiotics, prebiotics, and synbiotics to restore the healthy flora [7073]. Ley R.E., Backhed F., Turnbaugh P., Lozupone C.A., Knight R.D., Gordon J.I. It is obvious, then, that these are the taxa which comprise the core human gut pan-microbiome . The site is secure. Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. It is well established that gut microbes constantly interact among themselves and with the host tissues. It was indicated that CMC may influence the proportional composition of gut microbiota which utilize different PTS-related enzymes. 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. J-HY and L-DJ: data curation. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. Genus g_Anaerostipes is a branch of phylum Firmicutes, which is a dominant bacterial taxon in the human gut. Federal government websites often end in .gov or .mil. In addition, they found that despite considerable changes in the composition of the gut microbiota, the individual specific SNP variation pattern showed a temporal stability. 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. The ePub format uses eBook readers, which have several "ease of reading" features 2022 Jun 24;23(13):7020. doi: 10.3390/ijms23137020. 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]. (2018). MG-RAST (the Metagenomics RAST) server is an automated platform for the analysis of microbial metagenomes to get the quantitative insights of the microbial populations . attracting attention. WGS of the microbiota (e.g., Human Microbiome Project Consortium, 2012) is preferred over 16S rRNA-based analysis to elucidate taxonomic classification and bacterial diversity within members of the microbial community. (2022). We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service, and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled, A metagenomic study of the gut microbiome in Behcets disease. Importantly, metagenomic sequencing has unearthed a separate kingdom of resident viral species, many of which were unknown so far, constituting the gut virome [58]. Faust K., Raes J. Microbial interactions: from networks to models. 2013-1551G). Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. The degree, the closeness centrality, and the eigenvector centrality of s__Bacteroides_stercoris all changed a lot across groups. The association of CMC with p_Actinobacteria has not been reported before. Exploring the influence of the gut microbiota and probiotics on health: a symposium report. Nonetheless, some WGS-based unsupervised tools, such as TETRA [93], MetaCV [94], and PhyloPythia [95], are also available. The positive edge percentage was 74.61%, which indicated that most of these taxa had positive associations with others. Cows milk is conventionally considered to be beneficial. Elokil AA, Magdy M, Melak S, Ishfaq H, Bhuiyan A, Cui L, Jamil M, Zhao S, Li S. Animal. Unigenes of all samples were aligned according to the NCBI NR database2 using DIAMOND software with the lowest common ancestor algorithm. the display of certain parts of an article in other eReaders. Before Mason M. R., Preshaw P. M., Nagaraja H. N., Dabdoub S. M., Rahman A., Kumar P. S. (2015). 16S rRNA sequencing has indicated a decrease in Bacteroides and Firmicutes numbers in the colon and an increase in Enterobacteriaceae, such as adherent-invasive E. coli and other Proteobacteria in Crohns disease [60]. Bookshelf While the above findings need to be extended to diverse phenotypes (populations, diseases, age, etc. As shown in Figure 1, association of gut microbiota is highest with obesity followed by cancer. This may be one of the reasons why only two differential taxa are being replicated in the American cohort. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed. CMC, Cow milk consumption. 2019 Jan;63:54-61. doi: 10.1016/j.jnutbio.2018.09.016. 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. Bacterial composition in each group at different levels. All the subjects were divided into a control group (n = 248) and a CMC group (n = 146) according to their CMC status. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. Women in the postmenopausal stage usually suffered from many kinds of diseases, and some of them including osteoporosis and breast cancer were reported to be associated with gut microbiota (Zhu et al., 2018; Gatti and Fassio, 2019; Ozaki et al., 2021; Rettedal et al., 2021). Rawls J.F., Mahowald M.A., Ley R.E., Gordon J.I. CMC alters the functional potential of the gut microbiome. Am. Zhou S, Wang Z, He F, Qiu H, Wang Y, Wang H, Zhou J, Zhou J, Cheng G, Zhou W, Xu R, Wang M. J Nutr Biochem. (2017). To annotate functions to the sequences or genes, Kyoto Encyclopedia of Genes and Genomes (KEGG) organizes genes into KEGG enzymes, pathways, and orthologs appropriate for the elucidation of metabolic potential of the community. It enables the user to annotate multiple metagenomes at a time and also to compare the metabolic data [103]. and transmitted securely. Evolution of mammals and their gut microbes. found that the human gut microbiome is shared among family members, who have similar microbiota even if they live at different locations [4]. Filter-HUMAN is a tool for filtering human sequences from human microbiome samples.
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