scholarly journals Metatranscriptomic analysis of colonic microbiota’s functional response to different dietary fibers in growing pigs

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Jie Xu ◽  
Rongying Xu ◽  
Menglan Jia ◽  
Yong Su ◽  
Weiyun Zhu

Abstract Background Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis. Results The results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin. Conclusion The results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health.

2021 ◽  
Author(s):  
Jie Xu ◽  
Rongying Xu ◽  
Menglan Jia ◽  
Yong Su ◽  
Weiyun Zhu

Abstract BackgroundDietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expression profiles of the carbohydrate active enzymes (CAZymes) that respond to different types of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigated the functional response of colonic microbiota to different dietary fibers in pigs through metatranscriptomic analysis.ResultsThe results showed that the microbial composition and CAZyme structure of the three experimental groups changed significantly compared with the control group (CON). Based on a comparative analysis with the control diet, RPS increased the abundance of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella but decreased Sutterella; INU increased the relative abundance of Fusobacterium and Rhodococcus but decreased Bacillus; and PEC increased the relative abundance of the Streptococcus and Bacteroidetes groups but decreased Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated but that of GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; the gene expression of AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; and the gene expression of PL4, AA1, GT32, GH18, GH37, GH101 and GH112 downregulated but that of CE14, AA3, AA12, GH5, GH102 and GH103 upregulated in the PEC group. Compared with the RPS and INU groups, the composition of colonic microbiota in the PEC group exhibited more diverse changes with the variation of CAZymes and Streptococcus as the main contributor to CBM61, which greatly promoted the digestion of pectin.ConclusionThe results of this exploratory study provided a comprehensive overview of the effects of different fibers on nutrient digestibility, gut microbiota and CAZymes in pig colon, which will furnish new insights into the impacts of the use of dietary fibers on animal and human health.


2020 ◽  
Author(s):  
Jie Xu ◽  
Rongying Xu ◽  
Menglan Jia ◽  
Yong Su ◽  
Weiyun Zhu

Abstract Background Dietary fibers are widely considered to be beneficial for health by producing nutrients by gut microbial fermentation while helping with weight management and gut health. So far, the gene expression profiles of CAZymes responsing to different type of fibers (raw potato starch, RPS; inulin, INU; pectin, PEC) in the gut microbes of pigs are not well understood. Therefore, we investigate the functional response of colonic microbiota to different dietary fibers in pigs based on metatranscriptomic analysis. Results Results showed that the microbial composition and carbohydrate active enzymes (CAZymes) structure of three experimental groups changed significantly compared to the control group (CON). As determined by comparative analysis with the control diet, RPS increased the abundances of Parabacteroides, Ruminococcus, Faecalibacterium and Alloprevotella, and decreased Sutterella. INU increased the relative abundance of Fusobacterium and Rhodococcus, while decreased Bacillus. And pectin treatment increased the relative abundance of Streptococcus and Bacteroidetes group, while decreased the relative abundance of Clostridium, Clostridioides, Intestinibacter, Gemmiger, Muribaculum, and Vibrio. The gene expression of CAZymes GH8, GH14, GH24, GH38, GT14, GT31, GT77 and GT91 downregulated while GH77, GH97, GT3, GT10 and GT27 upregulated in the RPS diet group; AA4, AA7, GH14, GH15, GH24, GH26, GH27, GH38, GH101, GT26, GT27 and GT38 downregulated in the INU group; as to the PEC group, the gene expression of PL4, AA1, GT32, GH18, GH37, GH101, and GH112 downregulated while CE14, AA3, AA12, GH5, GH102 and GH103 upregulated. Compared to RPS and INU groups, the composition of colonic microbiota in the PEC group had more diverse changes with the variation of carbohydrate active enzymes and Streptococcus as the main contributor to CBM61, which promoted the digestion of pectin greatly. Conclusions The results of this exploratory study displayed a comprehensive overview on the effects of different fibers on gut microbiota and CAZymes in pig colons, which will provide new insights into the impacts of the use of dietary fibers on animal or human health.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qing Xia ◽  
Xiangtian Ling ◽  
Zhonghao Wang ◽  
Tao Shen ◽  
Minghao Chen ◽  
...  

Abstract Purpose and background Recently, we found that maximal medial rectus recession and lateral rectus resection in patients with complete lateral rectus paralysis resulted in a partial restoration of abduction. In an attempt to understand some of the mechanisms involved with this effect we examined gene expression profiles of lateral recti from these patients, with our focus being directed to genes related to myogenesis. Materials and methods Lateral recti resected from patients with complete lateral rectus paralysis and those from concomitant esotropia (controls) were collected. Differences in gene expression profiles between these two groups were examined using microarray analysis and quantitative Reverse-transcription PCR (qRT-PCR). Results A total of 3056 differentially expressed genes (DEGs) were identified between these two groups. Within the paralytic esotropia group, 2081 genes were up-regulated and 975 down-regulated. The results of RT-PCR revealed that PAX7, MYOG, PITX1, SIX1 and SIX4 showed higher levels of expression, while that of MYOD a lower level of expression within the paralytic esotropia group as compared with that in the control group (p < 0.05). Conclusion The decreased expression of MYOD in the paralytic esotropia group suggested that extraocular muscle satellite cell (EOMSCs) differentiation processes were inhibited. Whereas the high expression levels of PAX7, SIX1/4 and MYOG, suggested that the EOMSCs were showing an effective potential for differentiation. The stimulation resulting from muscle surgery may induce EOMSCs to differentiate and thus restore abduction function.


Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1374
Author(s):  
Bingbing Huang ◽  
Huangwei Shi ◽  
Li Wang ◽  
Lu Wang ◽  
Zhiqian Lyu ◽  
...  

This study was conducted to determine the effects of low-protein diet prepared with different levels of defatted rice bran (DFRB) and weight stages on growth performance and nutrient digestibility of growing–finishing pigs. The animal experiment included three stages. A total of 240 growing pigs with an initial body weight of 28.06 ± 8.56 kg for stage 1 were allocated to five diets including one control group and four DFRB diets supplemented with 2.5%, 5%, 7.5% and 10% DFRB, respectively. The 192 crossbred pigs with initial body weights of 55.03 ± 7.31 kg and 74.55 ± 9.10 kg were selected for stage 2 and stage 3, respectively. Pigs were allocated to four diets including one control group and three DFRB diets supplemented with 10%, 15% and 20% DFRB, respectively. The results showed that with the increase in DFEB intake, the gain: feed was linearly increased (p < 0.05), and the average daily feed intake tended to linearly decrease (p = 0.06) in stage 1. Except for the apparent total tract digestibility (ATTD) of acid detergent fiber (ADF) in stage 3, levels of DFRB had significant effects on the ATTD of gross energy (GE), dry matter (DM), ash, neutral detergent fiber (NDF) and ADF in three weight stages. In stage 1, with the increase in levels of DFRB, the ATTD of NDF and hemicellulose were firstly increased and then decreased (p < 0.01). In stage 2, with the increasing levels of DFRB, the ATTD of DM, ash and cellulose were firstly increased and then decreased (p < 0.01). In stage 3, the ATTD of GE, DM, ash, NDF and hemicellulose decreased linearly with the increase in levels of DFRB (p < 0.01). Collectively, DFRB could be used as a replacement for corns and soybean meal, and weight stage is important to consider when adjusting the additive proportion.


2018 ◽  
Vol 18 (4) ◽  
pp. 1007-1027 ◽  
Author(s):  
Małgorzata Świątkiewicz ◽  
Jerzy Księżak ◽  
Ewa Hanczakowska

AbstractThe aim of this experiment was to examine the possibility of replacing part of soybean meal in the diets of sows, their piglets and fatteners with two varieties of high- or low-tannin faba bean seed. Twenty-four sows were allocated to 3 groups, 8 animals in each. Control group (C) received standard feed mixture containing soybean meal as the main protein source. Next groups received standard feed mixture in which part of soybean meal was replaced by high-tannin variety Bobas (group HT) or low-tannin variety Kasztelan (group LT). Faba bean was added to diets at the level of 12 and 14% for pregnant and lactating sows, 6% for piglets, and 12 and 16% for fatteners (grower and finisher, respectively). Diets for half piglets and fatteners were supplemented with the enzyme Ronozyme VP. Apparent digestibility of nutrients was evaluated in a parallel experiment, using the same feeds on 18 barrows weighing about 40 kg (grower) and 80 kg (finisher). There was almost no difference in sow reproductive rates, litter weight and body weight of piglets on the first day of life were similar. Until 35 days of age piglets receiving faba bean grew faster than control ones. Control piglets grew fastest from 35 to 84 days of age, but differences were not significant. Enzyme supplement had a positive effect on body weight only from 56 to 84 days of piglet life. Digestibility of nutrients was lower in pigs fed with faba beans, especially in the grower period. Faba bean HT had lower nutrient digestibility in both periods of fattening. Almost all carcass traits were better in control pigs than in those fed with bean variety Bobas. Meat of these pigs had also the lowest content of unsaturated fatty acids and highest atherogenic indices. In sensory evaluation this meat had also the worst smell and taste. It can be stated that faba bean seeds, in moderate amounts, can partially replace soybean meal in feed for pigs, but some lowering of body weight gain and meat quality is possible especially when high-tannin varieties are used.


2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Chenlei Zheng ◽  
Cheng Wang ◽  
Tan Zhang ◽  
Ding Li ◽  
Xiao-feng Ni ◽  
...  

Objective. Posttransplantation diabetes mellitus (PTDM) is a known complication of transplantation that affects the prognosis. Tacrolimus (Tac or FK506) is a widely used immunosuppressant that has been reported to be a risk factor for PTDM and to further induce complications in heart and skeletal muscles, but the mechanism is still largely unknown. In our preliminary experiments, we found that after Tac treatment, blood glucose increased, and the weight of skeletal muscle declined. Here, we hypothesize that tacrolimus can induce PTDM and influence the atrophy of skeletal muscle. Methods. We designed preliminary experiments to establish a tacrolimus-induced PTDM model. Gene expression profiles in quadriceps muscle from this rat model were characterized by oligonucleotide microarrays. Then, differences in gene expression profiles in muscle from PTDM rats that received tacrolimus and control subjects were analyzed by using GeneSpring GX 11.0 software (Agilent). Functional annotation and enrichment analysis of differentially expressed genes (DEGs) helped us identify clues for the side effects of tacrolimus. Results. Our experiments found that the quadriceps in tacrolimus-induced PTDM group were smaller than those in the control group. The study identified 275 DEGs that may be responsible for insulin resistance and the progression of PTDM, including 86 upregulated genes and 199 downregulated genes. GO and KEGG functional analysis of the DEGs showed a significant correlation between PTDM and muscle development. PPI network analysis screened eight hub genes and found that they were related to troponin and tropomyosin. Conclusions. This study explored the molecular mechanism of muscle atrophy in a tacrolimus-induced PTDM model by bioinformatics analyses. We identified 275 DEGs and identified significant biomarkers for predicting the development and progression of tacrolimus-induced PTDM.


2019 ◽  
Vol 21 (1) ◽  
pp. 295
Author(s):  
Rebeca González-Fernández ◽  
Rita Martín-Ramírez ◽  
Deborah Rotoli ◽  
Jairo Hernández ◽  
Frederick Naftolin ◽  
...  

Sirtuins are a family of deacetylases that modify structural proteins, metabolic enzymes, and histones to change cellular protein localization and function. In mammals, there are seven sirtuins involved in processes like oxidative stress or metabolic homeostasis associated with aging, degeneration or cancer. We studied gene expression of sirtuins by qRT-PCR in human mural granulosa-lutein cells (hGL) from IVF patients in different infertility diagnostic groups and in oocyte donors (OD; control group). Study 1: sirtuins genes’ expression levels and correlations with age and IVF parameters in women with no ovarian factor. We found significantly higher expression levels of SIRT1, SIRT2 and SIRT5 in patients ≥40 years old than in OD and in women between 27 and 39 years old with tubal or male factor, and no ovarian factor (NOF). Only SIRT2, SIRT5 and SIRT7 expression correlated with age. Study 2: sirtuin genes’ expression in women poor responders (PR), endometriosis (EM) and polycystic ovarian syndrome. Compared to NOF controls, we found higher SIRT2 gene expression in all diagnostic groups while SIRT3, SIRT5, SIRT6 and SIRT7 expression were higher only in PR. Related to clinical parameters SIRT1, SIRT6 and SIRT7 correlate positively with FSH and LH doses administered in EM patients. The number of mature oocytes retrieved in PR is positively correlated with the expression levels of SIRT3, SIRT4 and SIRT5. These data suggest that cellular physiopathology in PR’s follicle may be associated with cumulative DNA damage, indicating that further studies are necessary.


2007 ◽  
Vol 19 (1) ◽  
pp. 213
Author(s):  
M. R. Park ◽  
I. S. Hwang ◽  
H. J. Moon ◽  
J. H. Shim ◽  
D. H. Kim ◽  
...  

Manipulations of early embryos require that the embryos be placed in vitro. The ability to reproduce in vivo conditions in vitro would greatly facilitate studies on the development of early embryos. A variety of different conditions have been described that result in development of pig embryos from the 1-cell stage to the blastocyst stage in vitro. There is a species-specific cell stage at which the early embryo is very sensitive to in vitro conditions, which generally corresponds to the stage at which the embryo begins producing significant amounts of RNA. The present study was conducted to investigate the relative amounts of apoptotic gene expression in miniature pig NT embryos under culture conditions of different osmolarity. Oocytes were cultured in TCM-199 for 40–44 h at 38.5�C under 5% CO2 in air. Miniature pig ear fibroblast cells were cultured to reach confluency, and the culture was continued for an additional 5–6 days. The NaCl group of embryos was cultured in PZM-3 supplemented with 138 mM NaCl in total concentration (280–320 mOsmol) for the first 2 days, and then cultured in PZM-3 (250–270 mOsmol) for a further 4 days. The control group of embryos was cultured in the PZM-3 for the entire period of in vitro culture. Total RNA samples were prepared from 2 blastocysts using the Roche 1st strand cDNA synthesis kit. Bax and Bcl-xl gene expression of blastocysts was analyzed by real-time RT-PCR. Developemntal rates were analyzed by a GLM procedure of SAS (SAS Institute, Inc., Cary, NC, USA). Relative gene expression was compared by Student&apos;s t-test. Blastocyst formation rate in the NaCl group was not different from that in the control group (25.4% and 23.2%, respectively), but the apoptosis rate was significantly lower (P &lt; 0.05) in the NaCl group (1.6%) than in the control (7.1%). The relative abundance of Bax mRNA expression was significantly higher (P &lt; 0.05) in the control group (n = 32) than in the NaCl group (n = 33). However, the relative abundance of Bcl-xl mRNA was significantly higher (P &lt; 0.05) in NaCl group. The relative abundance of Bax/Bcl-xl was significantly higher in the control group than in the NaCl group (P &lt; 0.05). These results indicate that the hypertonic culture condition at the early embryonic stage of miniature pig NT embryos could reduce the frequency of apoptosis through regulating Bax and Bcl-xl gene expression.


2010 ◽  
Vol 22 (1) ◽  
pp. 329
Author(s):  
C. L. V. Leal ◽  
S. Mamo ◽  
T. Fair ◽  
P. Lonergan

Once removed from the follicle, mammalian oocytes resume meiosis spontaneously and progress through breakdown of the germinal vesicle to the matured state at metaphase II. The ability to reversibly inhibit such meiotic resumption has been reported and is a potentially useful method for studying developmental competence acquisition in oocytes as well as in some cases allowing flexibility in an IVF system where oocytes are collected from distant locations or on different days. The aim of the present study was to determine the effect of temporary inhibition of meiotic resumption using the cyclin-dependent kinase inhibitor butyrolactone I (BLI) on gene expression in bovine oocytes. Immature bovine oocytes were recovered from the ovaries of slaughtered heifers at a commercial abattoir and assigned to 1 of 4 groups: (1) Control: immature oocytes were collected either immediately or (2) after IVM for 24 h in TCM-199 containing 10 ng mL-1 EGF and 10% (v/v) FCS, (3) Inhibited oocytes collected either 24 h after incubation in the presence of 100 μM BLI in TCM-199 with 3 mg mL-1 BSA or (4) after meiotic inhibition for 24 h followed by in vitro maturation. All cultures were carried out at 38.5°C under 5% CO2 in air and maximum humidity. For mRNA relative abundance analysis, cumulus cells were removed and pools of 10 denuded oocytes were snap frozen in liquid nitrogen and stored at -80°C until use. A total of 42 transcripts, previously reported to be related to cell cycle regulation and/or oocyte competence were evaluated by quantitative real time PCR. Differences in relative abundance were analyzed by ANOVA and Student’s t-test. The majority of transcripts were downregulated (P < 0.05) after IVM in control oocytes (23 out of 42) and the same pattern was observed in inhibited oocytes that were allowed to mature. Twelve transcripts remained stable (P > 0.05) after IVM in control oocytes; of these, only two (PTTG1 and INHBA) did not show the same pattern in inhibited and matured oocytes. Few genes (7) were upregulated after IVM in control oocytes (P < 0.05) and of these, three (PLAT1, RBP1, and INHBB) were not upregulated in inhibited oocytes after IVM. Inhibited oocytes showed similar levels of expression (P > 0.05) as immature control oocytes, except for two genes (LUM and INHBB), which were increased in these oocytes (P < 0.05). The expression profiles of cell cycle genes were mostly unaffected by the BLI treatment. The few genes affected were previously reported as competence-related and could be useful markers of oocyte competence following pretreatment. In conclusion, the changes occurring in transcript abundance during oocyte maturation in vitro were to a large extent mirrored following inhibition of meiotic resumption prior to IVM and subsequent release from inhibition and maturation. CLV Leal was supported by CNPq, Brazil (PDE 201487/2007-1); Supported by Science Foundation Ireland (07/SRC/B1156).


2020 ◽  
Vol 8 (5) ◽  
pp. 347 ◽  
Author(s):  
Izabela Michalak ◽  
Katarzyna Chojnacka ◽  
Daniel Korniewicz

In the present study, the effect of macroalga Enteromorpha sp. enriched with Zn(II) and Cu(II) ions on daily amounts of feces and urine excreted by growing pigs, apparent fecal nutrient digestibility and daily nitrogen balance and retention, meat quality and the slaughter value of carcasses was examined. The duration of feeding experiments was 87 days. In the control group, the requirement for zinc and copper was covered by inorganic salts, whereas in the experimental group algae enriched with these elements via biosorption were supplemented. No effect of Enteromorpha sp. on the increase in digestibility of dry matter, dry organic matter, crude protein, crude fat and nitrogen-free extractives was observed. Statistically significant differences concerned only the digestibility of crude ash. The daily amount of excreted feces and urine did not differ significantly between groups. Meat from pigs in the algal group was characterized by a lower water absorption and drip loss and contained less fat and more protein than meat from the control group. Furthermore, a slight darkening of the meat was observed. The weight of the liver was lower in pigs from the algal group. Enriched macroalga Enteromorpha sp. may be introduced into pig nutrition as a feed material as an alternative to inorganic salts.


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