IDCC 2201 metagenome sequencing for gut microbiome analysis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1055692 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:high throughput sequencing of the metagenome of mexican children
2020-03-16 | GSE143207 | GEO
Project description:Studies underestimate the microbial diversity and genotypic traits in the snails' microbiome. Caracolus marginella, a land snail native to Caribbean islands, can adapt to different environments. Our research focused on the generation of a metagenomic library from C. marginella gut, to further explore the diversity and functional traits. Thirty specimens of C. marginella were collected from the four regions of Puerto Rico. High molecular weight (40 kb) metagenomic libraries were generated using a direct DNA isolation method. DNA was end-repaired and ligated into a pCCFOS1 fosmid vector; then, the cloned DNA was transduced into Escherichia coli EPI300. The master pool library contains approximately 60,200 clones and restriction enzyme digestion showed that 90% of the library contains insert. After removing the fosmid and host genome sequences, 567,015 sequences were analyzed using the MG-RAST online server. The Bacteria domain was the most abundant (82.15%), followed by viruses (16.49%), eukaryotes (0.83%) and archaea (0.31%). The Proteobacteria (51.47%) was predominant in the gut environment, followed by unidentified virus (16.28%), and Actinobacteria (8.52%). Escherichia coli, Streptomyces avermitilis, and Burkholderia sp. were the most abundant species present. Subsystem functional analysis showed that 35.00% of genes belong to transposable elements, 10.00% of genes belong to clustering-based subsystems, 4.00% of genes belong to the production of cofactors and secondary metabolites, and 2.00% resistance to antibiotics and toxic compounds. The data generated in this research is the first metagenomic examination of a snail gut in Puerto Rico, and will serve as a baseline to start understanding of C. marginella gut microbiome.
| S-EPMC5734700 | biostudies-literature
Project description:Evidence is mounting that the gut-brain axis plays an important role in mental diseases fueling mechanistic investigations to provide a basis for future targeted interventions. However, shotgun metagenomic data from treatment-naïve patients are scarce hampering comprehensive analyses of the complex interaction between the gut microbiota and the brain. Here we explore the fecal microbiome based on 90 medication-free schizophrenia patients and 81 controls and identify a microbial species classifier distinguishing patients from controls with an area under the receiver operating characteristic curve (AUC) of 0.896, and replicate the microbiome-based disease classifier in 45 patients and 45 controls (AUC = 0.765). Functional potentials associated with schizophrenia include differences in short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters. Transplantation of a schizophrenia-enriched bacterium, Streptococcus vestibularis, appear to induces deficits in social behaviors, and alters neurotransmitter levels in peripheral tissues in recipient mice. Our findings provide new leads for further investigations in cohort studies and animal models.
| S-EPMC7109134 | biostudies-literature
Project description:Gut microbial β-glucuronidase (GUS) enzymes play important roles in drug efficacy and toxicity, intestinal carcinogenesis, and mammalian-microbial symbiosis. Recently, the first catalog of human gut GUS proteins was provided for the Human Microbiome Project stool sample database and revealed 279 unique GUS enzymes organized into six categories based on active-site structural features. Because mice represent a model biomedical research organism, here we provide an analogous catalog of mouse intestinal microbial GUS proteins-a mouse gut GUSome. Using metagenome analysis guided by protein structure, we examined 2.5 million unique proteins from a comprehensive mouse gut metagenome created from several mouse strains, providers, housing conditions, and diets. We identified 444 unique GUS proteins and organized them into six categories based on active-site features, similarly to the human GUSome analysis. GUS enzymes were encoded by the major gut microbial phyla, including Firmicutes (60%) and Bacteroidetes (21%), and there were nearly 20% for which taxonomy could not be assigned. No differences in gut microbial gus gene composition were observed for mice based on sex. However, mice exhibited gus differences based on active-site features associated with provider, location, strain, and diet. Furthermore, diet yielded the largest differences in gus composition. Biochemical analysis of two low-fat-associated GUS enzymes revealed that they are variable with respect to their efficacy of processing both sulfated and nonsulfated heparan nonasaccharides containing terminal glucuronides.IMPORTANCE Mice are commonly employed as model organisms of mammalian disease; as such, our understanding of the compositions of their gut microbiomes is critical to appreciating how the mouse and human gastrointestinal tracts mirror one another. GUS enzymes, with importance in normal physiology and disease, are an attractive set of proteins to use for such analyses. Here we show that while the specific GUS enzymes differ at the sequence level, a core GUSome functionality appears conserved between mouse and human gastrointestinal bacteria. Mouse strain, provider, housing location, and diet exhibit distinct GUSomes and gus gene compositions, but sex seems not to affect the GUSome. These data provide a basis for understanding the gut microbial GUS enzymes present in commonly used laboratory mice. Further, they demonstrate the utility of metagenome analysis guided by protein structure to provide specific sets of functionally related proteins from whole-genome metagenome sequencing data.
| S-EPMC6712278 | biostudies-literature
Project description:The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon vs. shotgun metagenomic sequencing techniques in 338 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.
| S-EPMC8320171 | biostudies-literature
Project description:Ruminant herbivores utilize a symbiotic relationship with microorganisms in their rumen to exploit fibrous foods for nutrition. We report the metagenome sequences of the greater kudu (Tragelaphus strepsiceros) rumen digesta, revealing a diverse community of microbes and some novel hydrolytic enzymes.
| S-EPMC4536684 | biostudies-literature
Project description:The amount of host DNA poses a major challenge to metagenome analysis. However, there is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire meaningful information from whole metagenome sequencing (WMS). Here, we evaluated the impact of a wide range of amounts of host DNA and sequencing depths on microbiome taxonomic profiling using WMS. Synthetic samples with increasing levels of host DNA were created by spiking DNA of a mock bacterial community, with DNA from a mouse-derived cell line. Taxonomic analysis revealed that increasing proportions of host DNA led to decreased sensitivity in detecting very low and low abundant species. Reduction of sequencing depth had major impact on the sensitivity of WMS for profiling samples with 90% host DNA, increasing the number of undetected species. Finally, analysis of simulated datasets with fixed depth of 10 million reads confirmed that microbiome profiling becomes more inaccurate as the level of host DNA increases in a sample. In conclusion, samples with high amounts of host DNA coupled with reduced sequencing depths, decrease WMS coverage for characterization of the microbiome. This study highlights the importance of carefully considering these aspects in the design of WMS experiments to maximize microbiome analyses.
| S-EPMC6581681 | biostudies-literature
Project description:Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. IMPORTANCE Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.
| S-EPMC9431278 | biostudies-literature
Project description:The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.
| S-EPMC11899681 | biostudies-literature
Project description:Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns. Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation. Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota, Candidatus Melainabacteria, Elusimicrobia, Firmicutes, Lentisphaerae, Proteobacteria, Tenericutes, and Verrucomicrobiota. Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.
| S-EPMC11684919 | biostudies-literature