Metagenomic insights into resistant starch degradation by human gut microbiota
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ABSTRACT:
PROVIDER: PRJEB25954 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2508880_1.fastq.gz | Fastqsanger.gz | |||
| ERR2508880_2.fastq.gz | Fastqsanger.gz | |||
| ERR2508890_1.fastq.gz | Fastqsanger.gz | |||
| ERR2508890_2.fastq.gz | Fastqsanger.gz | |||
| ERR2508900_1.fastq.gz | Fastqsanger.gz |
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Project description:Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.
| S-EPMC6238065 | biostudies-literature
Project description:Thermophilic fungus Myceliophthora thermophila with great capacity for polysaccharides degradation is attractive to be engineered into a cell factory to produce chemicals and biofuels directly from renewable polysaccharides such as starch. Understanding the molecular mechanism of starch degradation of the fungi would be helpful. To date, there has been no transcriptome analysis on starch in thermophilic fungi. In this study, we performed the transcriptomic profile of M. thermophila responding to soluble starch, and a 342-gene set was identified as “starch regulon”, including the major amylolytic enzyme (Mycth_72393), which was verified thereafter as the most important such hydrolase for starch degradation in this fungus. Moreover, the function of key amylolytic enzyme regulator AmyR in M. thermophila was evaluated by analyzing the performance of its deletion mutant using our CRISPR/Cas9 system, which showed significantly decreased amylase activity and poor growth on starch. Additionally, deletion of amyR led to resistance to carbon catabolite repression (CCR) and enhanced cellulases production. Our study provides an insight into understanding the molecular basis of starch degradation in this thermophilic fungus, and will accelerate the fungal strain rational engineering for starch-based biochemical production.
2021-02-02 | GSE110062 | GEO
Project description:Background Lytic polysaccharide monooxygenases (LPMOs) are often studied in simple models involving activity measurements of a single LPMO or a blend thereof with hydrolytic enzymes towards an insoluble substrate. However, the contribution of LPMOs to polysaccharide breakdown in complex cocktails of hydrolytic and oxidative enzymes, similar to fungal secretomes, remains elusive. Typically, two starch-specific AA13 LPMOs are encoded by mainly Ascomycota genomes. Here, we investigate the impact of LPMO loss on the growth and degradation of starches of varying resistance to amylolytic hydrolases by Aspergillus nidulans. Results Deletion of the genes encoding AnAA13A that possesses a CBM20 starch-binding module, AnAA13B (lacking a CBM20) or both AA13s genes resulted in reduction in growth on solid media with resistant, but not soluble processed potato starch. Larger size and amount of residual starch granules were observed for the AA13 KO strains as compared to the reference and the impairment of granular starch degradation was more severe for the AnAA13A KO based on a microscopic analysis. After five days of growth on raw potato starch in liquid media, the mount of residual starch was about 5-fold higher for the AA13 KO strains compared to the reference, which underscores the importance of LPMOs for degradation of especially resistant starches. Proteomic analyses revealed substantial changes in the secretomes of the AA13 double KO, followed by the AnAA13A deficient strains, whereas no significant changes in the proteome were observed for the AnAA13B deficient strain. Conclusions This study shows that the loss of AA13, especially the starch-binding AnAA13A, impairs degradation of resistant potato starch, but has limited impact less-resistant wheat starch and has no impact at all on processed solubilised starch. The effects of LPMO loss are more pronounced at the later stages of fungal growth, when the less-accessible regions of the substrate accumulate. The striking impact of the loss of a single LPMO against a whole secretome offers insight into the crucial role played by AA13 in the degradation of resistant starch and presents a methodological framework to analyse the contribution of distinct LPMOs towards complex substrates under in vivo conditions.
2020-09-02 | PXD020101 | Pride
Project description:An Arabidopsis double mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial Glucan phosphorylase (PHS1) revealed a unique starch metabolism. Dpe2/phs1 was reported to have a dwarf growth phenotype, an uneven starch distribution in the rosettes, and a strongly reduced starch granule number per chloroplast when grown under diurnal rhythm. Here we analyzed dpe2/phs1 in more detail and found that it showed three distinct growth periods. In young plants the starch granule number was similar to Col-0, then the starch granule number decreased massively down to one or no granule per chloroplast followed by an increase of the granule number. Thus, in dpe2/phs1 the control over the starch granule number is impaired and it is not defective in starch granule initiation. The data also show that the granule number is not fixed and is regulated over the entire plant growth. Further, also the chloroplasts revealed alterations during these three periods with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism perpetuated if starch degradation is further impaired by additionally lack of Isoamylase 3 and Starch excess 4. Transcriptomic studies and metabolic profiling of dpe2/phs1 revealed a gene co-regulation of most starch metabolism related genes and a clear metabolic separation. Further most senescence-induced genes were found to up-regulated more than 2-fold in the starch-less mature leave. Thus, dpe2/phs1 is a unique source to understand especially the starch granule number regulation in detail. We performed gene expression profiling analysis using data obtained from RNA-seq of 3 stages from both Col-0 and dpe2/phs1.
2022-05-23 | GSE201804 | GEO
Project description:Purpose: The ∆col-26 mutant cannot utilize starch components and many other simple sugars efficiently. We employed RNA-seq based transcriptome profiling to reveal genes under the control of col-26. Method: We first obtained transcriptional data of Neurospora crassa WT on Vogel's minimal medium (VMM) without carbon source, on VMM with 2% sucrose, and on VMM with starch component, and transcriptional data of the ∆col-26 mutant on VMM with maltose or amylose. Results: We identified a starch-regulon of 322 genes and found that 255 of the starch-regulon were down regulated in in absence of col-26. We also found that genes with functions in primary carbon and nitrogen metabolism and amino acid biosynthesis were also down regulated in the mutant. Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different starch components and identify COL-26 as a critical regulator in both starch degradation and primary carbon and nitrogen regulation.
2017-04-09 | GSE92848 | GEO
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out 48 dye-swap - CATMA arrays
2011-03-01 | E-GEOD-20964 | biostudies-arrayexpress
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out 48 dye-swap - CATMA arrays
2011-05-12 | E-GEOD-21793 | biostudies-arrayexpress
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out
2011-05-12 | GSE21793 | GEO
Project description:gnp06-02_starch - isd-starch - What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves. - comparison between several mutant of the starch biosynthesis and the WT, at the end of the day and at the end of the night Keywords: gene knock out
2011-03-01 | GSE20964 | GEO
Project description:Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
| PRJEB22786 | ENA