about navigating our updated article layout. Annotated taxonomy units within the phyla of Firmicutes (A), Actinobacteria (B), and Proteobacteria (C) were visualized in terms of relative abundance and taxonomic hierarchy for normal (left) and obese (right) cat gut microbiome. The eight normal and eight obese cat microbiomes formed two distinct groups when unsupervised clustering was performed using the relative abundance of the top 20 genera (Fig. In conclusion, we discovered dramatically decreased microbial diversity in obese cat gut microbiota, suggesting potential dysbiosis. Furthermore, the gut microbiota influences drug effectiveness because of its effects on drug metabolism7,8. Compared with the obese cat microbiota from 6-year males, the normal cats formed a cluster, which was well separated from the obese cat microbiota (Fig. Despite the large difference in genome length, the average length of each gene was similar (Fig. We then compared the full-length 16s rRNAs of these genomes with those of related bacterial strains, and found that the differences between them were small (Fig. 2018. performed the experiments; X.M., E.C.G., W.C., and X.W. Chung YW, Gwak HJ, Moon S, Rho M, Ryu JH. Here, we report on the influence of host genetics on the gut microbiome in IBD. (A) Bar plot of the body condition scores of normal and obese cats in this study. An important question remains: what matters to human health: the quality or quantity of microbes45? No antibiotic treatments were applied to any of these cats within 2 months prior to the study. At a false discovery rate (FDR) of 10% and relative abundance of 0.5% or higher, 17 genera have a log2 fold change greater than 2 (Fig. 4B), and family levels (Erysipelotrichaceae and Acidaminococcaceae, respectively; Fig. Microbial whole-genome resequencing involves sequencing the entire genome of a bacteria, virus, or other microbe, and comparing the sequence to that of a known reference. The beta-diversity analysis also revealed a distinct separation of the normal and obese cat microbiomes. Lactimicrobium massiliense gen. nov., sp. School of Life Sciences and Technology, Tongji University, Shanghai, China, c In the obese cat microbiome, we discovered a significant reduction in microbial diversity (P<0.01) and Firmicutes abundance (P=0.005), as well as decreased Firmicutes/Bacteroidetes ratios (P=0.02), which is the inverse of obese human/mouse microbiota. (E) High abundant bacterial species (relative abundance>0.5%) with high-fold change (>16) between normal (green) and obese (yellow) cat gut microbiota. Second, although we established an effective method, it is still not easy to acquire sufficient high quality genomic DNA, and we only harvested two samples. Based on the protein sequence homology to the CAZy database, we detected 105 CAZy families (Data set S8), which were assigned to 51 glycoside hydrolases (GHs), 38 glycosyltransferases (GTs), seven carbohydrate-binding modules (CBMs), six polysaccharide lyases (PLs), two carbohydrate esterases (CEs), and one auxiliary activities (AA). Would you like email updates of new search results? (C). The body condition score (BCS) and body weight were measured for cats in this study (Table S1). Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. The non-redundant assembly contains 355,573 microbial contigs, with a total length of 961,105,174bp (N50=11,097bp). Mukherjee S, et al. In addition to the taxonomy level, the reduced diversity was also observed at the gene level, in which the number of microbial genes predicted in the obese microbiome (598,349) was significantly fewer than the normal cat microbiome (912,251). 2013. The whole-exome sequencing (WES) is a less expensive but still effective alternative to whole-genome sequencing (WGS). Marsilio S, Pilla R, Sarawichitr B, Chow B, Hill SL, Ackermann MR, Estep JS, Lidbury JA, Steiner JM, Suchodolski JS. Generally, gut microbiota maintains dynamic balancing when our bodies function well. A total of 400 bacteria species were significantly enriched in the obese cat gut microbiome, at an FDR of 10% and log2 fold change of 2 or more (Data set S5). (D). X.W., E.C.G., and D.R.M. However, until now this research has almost exclusively used 16S rRNA amplicon (16S) sequencing. The libraries were measured by qPCR before being sequenced on an Illumina NovaSeq6000 sequencing machine with 150-bp paired-end reads at the Genomics Service Laboratory at the HudsonAlpha Institute for Biotechnology (Huntsville, AL). collected samples and extracted the bacteria genome DNA. No significant changes were detected at the phylum level for Proteobacteria or Actinobacteria (Fig. The HMP Unified Metabolic Analysis Network, HUMAnN 3.0 (110), was used to profile the abundance of microbial metabolic pathways from metagenomic sequencing data based on MetaCyc database (111). (Fig.5d).5d). When the individual CAZyme families were investigated, we discovered a significant decrease in the carbohydrate-binding module CBM50 and Glycosyltransferase GT25 in obese cat gut microbiota. (A, Top 20 abundant bacterial genera and species in cat gut microbiota, and their, Significant differences in taxonomic abundance, Significant differences in taxonomic abundance that discriminate normal and obese cat gut microbiome, MAG genome quality assessment, normal and obese microbiota coverage, and syntenic analysis of, Krona plots reflecting the phylogenetic relationship and composition changes in Firmicutes, Actinobacteria, and, Quantitative PCR validation of seven indicator bacterial species enriched or depleted in the, Significantly altered metabolic pathways and, Significantly altered metabolic pathways and CAZy families in obese and normal cat gut, MeSH Last but not least, fecal sample collection methods also affect the results of microbiome analysis. With the continuous development of TGS technology, it is probable that more sequencing data can be acquired in a single sample. (Fig.2a)2a) and 12 were more than 99% complete (Fig. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. (B) Heatmap of relative frequency for the top 20 most abundant Campylobacter species. The key bacterial community and functional capacity alterations discovered from this study will inform new weight management strategies for obese cats, such as evaluations of specific diet formulas that alter the microbiome composition, and the development of prebiotics and probiotics that promote the increase of beneficial species and the depletion of obesity-associated species. 2009. I find it especially interesting that you are using it to categorize the microbes inside the human gut. The role of gut microbiota in the development of obesity and diabetes. Factors associated with overweight cats successfully completing a diet-based weight loss programme: an observational study, Revised estimates for the number of human and bacteria cells in the body. It is mandatory to procure user consent prior to running these cookies on your website. With this greatly improved set of genomic blueprints in hand, we will undoubtedly be able to advance our understanding of how the microbiome influences health and disease. This website uses cookies to improve your experience while you navigate through the website. It had 2111 genes, 12 rRNAs, and 63 tRNAs (Fig. Interestingly, Prevotella copri has a significantly higher abundance in fat pigs, and was shown to promote host chronic inflammation, intestinal permeability, lipogenesis, and fat accumulation through the TLR4 and mTOR signaling pathways (83). Metagenome assembly was performed with flye software after obtaining valid reads. Get free reports and resources from our world class speakers. Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses. 2022 Jun 29;10(3):e0083722. 4C, ,E),E), with a 20-fold increase in the obese microbiome from 0.11% to 2.27% (TableS8 and Fig. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Huerta-Cepas J, Szklarczyk D, Heller D, Hernndez-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. 2019. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5,090 organisms and 2,502 viruses. Weight gain after fecal microbiota transplantation in a patient with recurrent underweight following clinical recovery from anorexia nervosa. As an important aspect of microbiome function, carbohydrate-active enzymes (CAZymes) are responsible for the synthesis and breakdown of complex carbohydrates in the cat gut microbiome. performed microbiome analysis. Philip recently gave a keynote presentation at 3rd Microbiome R&D and Business Collaboration Congress: Asia. Keywords: The top 20 most abundant bacterial genera and species were listed in TableS4 and TableS5. Another study in 2019 contrasting the microbiomes of diabetic and control cats found no effect of breed, sex, or age on the gut microbial communities (54). Careers. Compared with the metagenome, genes in the microbial genome have traditionally been underestimated. National Library of Medicine Interestingly, the 16S sequence in contig_511 had fewer differences than that in Escherichia coli ({"type":"entrez-nucleotide","attrs":{"text":"U00096.3","term_id":"545778205","term_text":"U00096.3"}}U00096.3) (Supplementary Fig. SFAs can add to the risk of cardiovascular disease by increasing the low-density lipoprotein (LDL) cholesterol levels in the serum. Chiang C-F, Villaverde C, Chang W-C, Fascetti AJ, Larsen JA. 2017, 30(4): 1015. To assess the statistical significance of the differential abundance of genera or species in normal cats and obese cats, Mann-Whitney U tests (105) were performed in R (Data set S5, S6). What is Net Zero and what does it mean for events? There are two main methods for bacteria metagenome sequencing: 16S rRNA-based sequencing and whole-metagenome shotgun sequencing (WGS). Therefore, Bifidobacterium is often used as probiotics to reduce gut problems such as diarrhea or constipation, and it was shown to have an impact on obesity. 2009. Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P. 2018. 8600 Rockville Pike Top 20 abundant bacterial genera and species in cat gut microbiota, and their relationship to cat obesity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. 1003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Bethesda, MD 20894, Web Policies Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. In addition, the appearance or over-proliferation of parasitic microbes could also be the unignorable inducement for the breakdown of community stability and the reason for jeopardizing our health, making it pivotal to study certain disease-related microbes and their relationship between human. Microbiota and SCFA in lean and overweight healthy subjects. Major gut microbiota members utilise different strategies for gut colonisation and high oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation. Saeculare (Fig. Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. PMC legacy view High-quality filtered reads were then mapped to the feline reference genome (GCF_000181335.3) using Burrows-Wheeler Aligner (BWA) (v0.7.17-r1188) (92) and SAMtools (v1.6) (93). Before 2022. Discovering event sustainability in Brussels. Linear discriminant analysis and quantitative PCR (qPCR) validation revealed significant increases of Bifidobacterium sp., Olsenella provencensis, Dialister sp.CAG:486, and Campylobacter upsaliensis as the hallmark of obese microbiota among 400 enriched species, whereas 1,525 bacterial species have decreased abundance in the obese microbiome. The filtered PE reads from each metagenome were aligned to the assembled cat reference metagenomic contigs (TableS2). d Function analyses of all the CDSs of the two samples. Whole-genome de novo sequencing refers to sequencing a novel genome with no requirement of reference sequences, which allows for culture-independent sophisticated analysis and sampling of gut microorganisms. We analyzed the data of prokaryotes genomes in the NCBI database and found that complete genomes account for only a small portion (https://www.ncbi . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, CD-HIT: accelerated for clustering the next-generation sequencing data, Ab initio gene identification in metagenomic sequences, Fast and sensitive taxonomic classification for metagenomics with Kaiju. (Fig.4a).4a). We emptied the catch tube and added 500L of prepared wash buffer #2 to the SPIN filter tube and gently resuspended the pellet. Single bacteria analyses included gene prediction, non-coding RNA (ncRNA) prediction, repeat sequence prediction, nonredundant analysis, and common function potential analyses. Long-term diet quality and gut microbiome functionality: a prospective, shotgun metagenomic study among urban Chinese adults. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, OHara R, Simpson G, Solymos P, Stevens M, Wagner H. 2013. and transmitted securely. 4C, ,6A, 6A, and Table S7), with an average depth of >200 across the entire genome in the normal microbiome but zero coverage in the obese microbiome (Fig. In contrast, C. helveticus, was extremely low in abundance in the obese microbiome (0.02%), but with a 12-fold increase in the normal microbiome. These previous studies identified phylum and genus level changes in the obese cat microbiome, but failed to discover bacterial species-level changes in the feline gut microbiota. Methylcitrate cycle I and II, as well as the biosynthesis of glutamine and arginine amino acids were also enriched compared with the obese cat gut microbiome (Fig. Effects of obesity on lipid profiles in neutered male and female cats. b Complete analysis of the contigs in the two samples. 5C). (A, B) Heatmap of relative frequency for the top 20 most abundant bacteria genera (A) and species (B). analyzed and interpreted the data. Fecal samples were collected under sedation immediately after blood collection to prevent interference of epinephrine-mediated hyperglycemia (TableS1). Our inability to culture this bacterium has limited our understanding of its ecological role in the intestinal environment and its relation to humans health. (C) Syntenic region plot of Erysipelotrichaceae bacterium AU001MAG with its two most related species, Lactimicrobium massiliense and Bulleidia sp. PLoS One. The gut microbiota portrays a specific microbial community and has been identified with great significance towards human health. There are no available licensed drugs for treating feline obesity, and classic interventions for weight loss such as calorie restrictions and physical exercise are often challenging and are ultimately ineffective (8). Conversely, being overweight or obese can cause dysbiosis, often associated with low microbial diversity and richness in gut microbiota (27,29). Afterwards, we centrifuged the samples at 14,000 g twice to extract residual ethanol. 3a, b). The gut microbiota associations with feline obesity had been studied in the context of age, diet, neutering, and diabetic status (32, 48, 53, 54). Herein, we performed a deep shotgun met We isolated and purified the gut microbiota genome DNA with a DNA purification kit. (G to K) Box plots of frequency for the five most abundant phyla: Firmicutes (G), Bacteroidetes (H), Fusobacteria (I), Proteobacteria (J), and Actinobacteria (K). The authors declare no conflict of interest. At the microbial metabolic pathway level (Data set S7), we identified 10 pathways significantly enriched in abundance in the obese cat gut microbiome (log2FC>1.5, FDR<0.1), while 11 pathways were significantly depleted (log2FC < 1.5, FDR<0.1; Data set S7). The checkM genome completeness was 96.2% (Fig. Among the obese microbiome enriched pathways, eight out of 10 were biosynthesis pathways. Evaluation of a nine-point body condition scoring system in physically inactive pet cats, Development and validation of a body condition score system for cats: a clinical tool.
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