Addition of insoluble fiber to isolation media allows for increased diversity of lab-cultivable microbes derived from gut samples IDBAC FILES
Ontology highlight
ABSTRACT:
INSTRUMENT(S): autoflex
ORGANISM(S): Mixed Libraries (ncbitaxon:590738)
SUBMITTER: 
Laura Sanchez
PROVIDER: MSV000084064 | MassIVE | Fri Jul 05 15:45:00 BST 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:There is a gap in measured microbial diversity when comparing genomic sequencing techniques versus cultivation from environmental samples in a laboratory setting. Standardized methods in artificial environments may not recapitulate the environmental conditions that native microbes require for optimal growth. For example, the intestinal tract houses microbes at various pH values as well as minimal oxygen and light environments. These microbes are also exposed to an atypical source of carbon: dietary fiber compacted in fecal matter. To investigate how the addition of insoluble fiber to isolation media could affect the cultivation of microbes from zebrafish intestines, an isolate library was built and analyzed using the bioinformatics pipeline IDBac. While all isolation media encouraged the growth of species from several phyla, the extent of growth was greater with the addition of fiber allowing for easier isolation. Furthermore, fiber addition altered the metabolism of the cultivated gut-derived microbes and induced the production of unique metabolites that were not produced when microbes were otherwise grown on standard isolation media. Addition of this inexpensive carbon source to the media supported the cultivation of a diverse community whose secondary metabolite production may more closely replicate their metabolite production in vivo.
| S-EPMC7524352 | biostudies-literature
Project description:This is the raw MALDI-TOF protein and small molecule data collected on 82 bacterial isolates cultivated from the intestines of zebrafish.
2019-07-05 | MSV000084061 | MassIVE
Project description:Previous study found that appropriate high-fiber diet (containing 19.10% total dietary fiber [TDF], treatment II) did not reduce apparent fiber digestibility of Chinese Suhuai finishing pigs and increased the yield of short-chain fatty acids (SCFAs), but too high-fiber diet (containing 24.11% TDF, treatment IV) significantly reduced apparent fiber digestibility compared with normal diet (containing 16.70% TDF, control group). However, characteristics of microbiota at the species level and histological structure in pigs with the ability to digest appropriate high-fiber diets were still unknown. This study conducted comparative analysis of cecal physiology and microbial populations colonizing cecal mucosa. The results showed intestinal development indexes including cecum length, densities of cecal goblet cells, and renewal of cecal epithelial cells in treatment II and IV had better performance than those in the control. Paludibacter jiangxiensis, Coprobacter fastidiosus, Bacteroides coprocola CAG:162, Bacteroides barnesiae, and Parabacteroides merdae enriched in treatment II expressed large number of glycoside hydrolase (GH)-encoding genes and had the largest number of GH families. In addition, pathogenic bacteria (Shigella sonnei, Mannheimia haemolytica, and Helicobacter felis) were enriched in treatment IV. Correlation analysis revealed that the intestinal development index positively correlated with the relative abundance of cecal mucosal microbiota and the amount of digested fiber. These results indicated that increased proportions of fiber-degrading microbes and enhanced intestinal development jointly promote the host to digest an appropriate high-fiber diet. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. IMPORTANCE Although studies about the effects of dietary fiber on fiber digestion and intestinal microbiota of pigs were widely in progress, few studies have been conducted on the dynamic response of intestinal microbiota to dietary fiber levels, and the characteristics of intestinal microbiota and intestinal epithelial development adapted to high-fiber diet s were still unclear. Appropriate high fiber promoted the thickness of large intestine wall, increased the density of cecal goblet cells, and promoted the renewal of cecal epithelial cells. In addition, appropriate high fiber improves the microbial abundance with fiber-digesting potential. However, excessive dietary fiber caused an increase in the abundance of pathogenic bacteria. These results indicated that an increased proportion of fiber-degrading microbes and enhanced intestinal development jointly promote host to digest appropriate high-fiber diets. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. Our data provided a theoretical basis for rational and efficient utilization of unconventional feed resources in pig production.
| S-EPMC9948726 | biostudies-literature
Project description:The experimental objective was to investigate the impact of xylanase on the bioavailability of energy, oxidative status, and gut function of growing pigs fed a diet high in insoluble fiber and given a longer adaptation time than typically reported. Three replicates of 20 gilts with an initial body weight (BW) of 25.43 ± 0.88 kg were blocked by BW, individually housed, and randomly assigned to one of four dietary treatments: a low-fiber control (LF) with 7.5% neutral detergent fiber (NDF), a 30% corn bran without solubles high-fiber control (HF; 21.9% NDF), HF + 100 mg/kg xylanase (HF + XY; Econase XT 25P), and HF + 50 mg/kg arabinoxylan-oligosaccharide (HF + AX). Gilts were fed ad libitum for 36 d across two dietary phases. Pigs and feeders were weighed on days 0, 14, 27, and 36. On day 36, pigs were housed in metabolism crates for a 10-d period, limit fed (80% of average ad libitum intake), and feces and urine were collected the last 72 h to determine the digestible energy (DE) and metabolizable energy (ME). On day 46, serum and ileal and colonic tissue were collected. Data were analyzed as a linear mixed model with block and replication as random effects, and treatment, time, and treatment × time as fixed effects. There was a significant treatment × time interaction for BW, average daily gain (ADG), and gain to feed (G:F; P < 0.001). By design, BW at day 0 did not differ; at day 14, pigs fed LF were 3.5% heavier, and pigs fed HF + XY, when compared with HF, were 4% and 4.2% heavier at days 27 and 36, respectively (P < 0.001). From day 14 to 27 and day 27 to 36, when compared with HF, HF + XY improved ADG by 12.4% and 10.7% and G:F by 13.8% and 8.8%, respectively (P < 0.05). Compared with LF, HF decreased DE and ME by 0.51 and 0.42 Mcal/kg, respectively, but xylanase partially mitigated that effect by increasing DE and ME by 0.15 and 0.12 Mcal/kg, over HF, respectively (P < 0.05). Pigs fed HF + XY had increased total antioxidant capacity in the serum and ileum (P < 0.05) and tended to have less circulating malondialdehyde (P = 0.098). Pigs fed LF had increased ileal villus height, and HF + XY and HF + AX had shallower intestinal crypts (P < 0.001). Pigs fed HF + XY had increased ileal messenger ribonucleic acid abundance of claudin 4 and occludin (P < 0.05). Xylanase, but not AX, improved the growth performance of pigs fed insoluble corn-based fiber. This was likely a result of the observed increase in ME, improved antioxidant capacity, and enhanced gut barrier integrity, but it may require increased adaptation time to elicit this response.
| S-EPMC7392531 | biostudies-literature
Project description:The main purpose of the present study was to assess the effect of soluble and insoluble fiber on colonic bacteria and intestinal barrier function in a piglet model. A total of 24 piglets (25 ± 1 d old; 7.50 ± 0.31 kg) were randomly allotted to 4 treatments: basal diet (control, CON), 1% insoluble dietary fiber (IDF) diet, 1% soluble dietary fiber (SDF) diet, and 0.5% insoluble fiber + 0.5% soluble dietary fiber (MDF) diet. The trial lasted 28 days. SDF-fed piglets showed a higher (P < 0.05) bacterial a-diversity (observed_species, chao1, and ACE) and a higher relative abundance of Proteobacteria and Actinobacteria, Solobacterium, Succinivibrio, Blautia, and Atopobium in colonic digesta than CON, IDF, and MDF groups (P < 0.05). At the same time, Bacteroidetes, Euryarchaeota, Phascolarctobacterium, Coprococcus_1, and Prevotella_1 were significantly increased in the IDF group when compared with CON, SDF, and MDF groups (P < 0.05). Furthermore, Bacteroidetes and Enterobacteriaceae, Selenomonas, Phascolarctobacterium, and Alloprevotella(P < 0.05) were significantly higher in the MDF group than those in the other three groups (P < 0.05). SDF diet increased the concentrations of short-chain fatty acid (SCFA) in colonic digesta (P < 0.05) when compared with the CON group and enhanced weight index of the colon (P < 0.05) than the CON and IDF groups. Furthermore, compared with the CON group, SDF, IDF, and MDF diets all upregulated the mRNA expressions of claudin-1 (CLDN-1) in colonic mucosa (P < 0.05), SDF and IDF diets upregulated the mRNA expressions of mucin 2 (MUC2) (P < 0.05), SDF diet increased mRNA expressions of zonula occludens 1 (ZO-1) and occludin (OCLN), while the IDF group enhanced the secretory immunoglobulin A (sIgA) concentrations (P < 0.05), respectively. IDF and MDF diets decreased expressions of TNF-α(P < 0.05). We concluded that the influence of soluble fiber on colonic microbiota was more extensive than that of insoluble fiber. Moreover, soluble fiber could more effectively improve colonic barrier function by upregulating gene expressions of the gut barrier.
| S-EPMC6944961 | biostudies-literature
Project description:Extensive research in recent years into the use of various fiber sources in poultry nutrition has led to the perception that dietary fiber is more than a simple diet diluent. Several studies showed that the feeding of insoluble fiber sources such as oat hulls, sunflower hulls or wood shavings may affect digestive physiology and function improving chickens health and growth performance. In this context, the effect of lignocellulose as an insoluble dietary fiber source is increasingly being investigated. Lignocellulose is a component of plant cell walls and consists mainly of the insoluble carbohydrate polymers cellulose and hemicelluloses as well as the phenolic polymer lignin. Lignocellulose is chemically and physicochemically different from other insoluble fiber sources and thus possibly has different effects on poultry compared to traditional fiber sources. Several studies investigated the effect of dietary lignocellulose on growth performance, nutrient digestibility, gastrointestinal tract development and intestinal microbiota in broilers and laying hens. Studies differed in terms of feed formulation and lignocellulose inclusion level as well as products of different suppliers were used. The results obtained are inconsistent; beneficial, indifferent or detrimental effects of feeding lignocellulose were observed, so that a final assessment of lignocellulose as a "novel" insoluble fiber source is difficult. This review article summarizes the results of studies in connection with the feeding of lignocellulose to poultry, compares them with those that have used other insoluble fiber sources and illuminates the possible mechanisms of action.
| S-EPMC8212492 | biostudies-literature
Project description:We investigated which microbial taxa in coastal Red Sea water were stimulated by addition of mucus from the coral Fungia sp. Decreases in the concentration and C/N ratio of particulate organic material during short-term incubations (50 h) were paralleled by a steep rise in the number of Gammaproteobacteria, particularly Alteromonadaceae, followed by Vibrionaceae. Two almost identical genotypes affiliated with Alteromonas macleodii accounted for up to >85% of all Alteromonadaceae (45% of the total cells) in the mucus-amended enrichments but were rare in unamended control incubations and in ambient seawater. A. macleodii-like bacteria might thus be important in the transfer of organic carbon from coral mucus to the pelagic microbial food webs of coral reefs.
| S-EPMC2394949 | biostudies-literature
Project description:Modified okara insoluble dietary fiber (OIDF) has attracted great interest as a promising Pickering emulsifier. At present, the modification methods are mainly physicochemical methods, and the research on microbial modified OIDF as stabilizer is not clear. In this work, modified OIDF was prepared by yeast Kluyveromyces marxianus fermentation. The potential of modified OIDF as a Pickering emulsifier and the formation and stability of OIDF-Pickering emulsions stabilized by modified OIDF were characterized, respectively. The results showed that the specific surface area, hydrophilicity, and electronegativity of the modified OIDF were all enhanced compared with the unmodified OIDF. The existence of the network structure between droplets is the key to maintain the stability of the emulsions, as indicated by Croy-Scanning Electron Microscope (Croy-SEM) and rheological properties measurements. The stability of OIDF-Pickering emulsions was evaluated in terms of storage time, centrifugal force, pH value, and ionic strength (NaCl). Moreover, the OIDF-Pickering emulsions stabilized by modified OIDF showed better stability. These results will contribute to the development of efficient OIDF-based emulsifiers, expand the application of emulsions in more fields, and will greatly improve the high-value utilization of okara by-products.
| S-EPMC8700857 | biostudies-literature
Project description:Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. We demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested -50 to -400 mV vs. Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to -295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications.
| S-EPMC4294203 | biostudies-literature
Project description: Not available
| S-EPMC8375075 | biostudies-literature