Relative Abundance Of Ruminococcaceae Research Articles

Effects of different molecular weights of chitosan on methane production and bacterial community structure in vitro

As a new feed additive, chitosan has been shown in recent years to have a certain role in reducing methane emissions from the gastrointestinal tracts of ruminants. However, the effects of chitosan with different molecular weights on rumen fermentation, methane production and bacterial community structure are not yet clear. A basal diet without chitosan served as the control (CTL), and the treatment diets were supplemented with chitosan with different molecular weights: 1 000 (1K), 3 000 (3K), 5 000 (5K), 50 000 (5W) and 200 000 (20W) dry matter (DM). Six fermentation units per treatment were established. Gas chromatography was used to measure the concentrations of methane, H2 and volatile fatty acids (VFAs). The bacterial 16S rRNA genes were sequenced with an Illumina MiSeq platform and analysed to reveal the relative abundances of bacterial community taxa. The results showed that the propionate proportion was significantly increased by the addition of chitosan with different molecular weights (P<0.05), while methane production and the acetate proportion were significantly decreased (P<0.05). The relative abundances of Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG_003 were significantly increased in the 3K chitosan group compared with the CTL group, whereas the relative abundance of Ruminococcaceae_NK4A214_group was significantly decreased (P<0.05). Correlation analyses of the relative abundances of the bacterial genera showed that Prevotella was positively related to propionate production (P<0.05). In conclusion, 3K chitosan could reduce methane production by replacing fibrolytic bacteria (Firmicutes and Fibrobacteres) with amylolytic bacteria (Bacteroidetes and Proteobacteria) in the bacterial community structure.

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice

Fine particulate matter (PM2.5) have become a major public health concern because of their adverse effects on health. Lungs are considered the primary organ affected by PM2.5. In order to understand the mechanism underlying PM2.5-induced lung injury, 16S rRNA gene sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis were conducted to investigate the impact of PM2.5 exposure on lung microbiome and its metabolic profile. Mice were exposed to PM2.5 through intratracheal instillation and a lung injury model was established. 16S rRNA gene sequencing indicated that PM2.5 exposure significantly altered the richness, evenness, and composition of the lung microbiome. Metabolomics profiling showed that the levels of lung metabolites were perturbed after PM2.5 exposure. The altered metabolites mainly belonged to metabolic pathways, such as the citrate cycle, glyoxylate and dicarboxylate metabolism, pyruvate metabolism, purine and pyrimidine metabolism, and valine, leucine, and isoleucine metabolism. The altered lung microbiota showed significant correlations with lung metabolites. The levels of fumaric acid negatively correlated with the relative abundance of Ruminococcaceae, Enterobacteriaceae, and Pseudomonadaceae. These results revealed that PM2.5 exposure not only significantly altered the lung microbiome composition but also perturbed a number of metabolites involved in diverse metabolic pathways. This study improves our understanding of the mechanism of lung injury after PM2.5 exposure.

Sturgeon hydrolysates alleviate DSS-induced colon colitis in mice by modulating NF-κB, MAPK, and microbiota composition.

Sturgeon muscle byproduct collected after caviar production is usually not fully utilized, and sometimes may be discarded, thus causing a lot of waste. Yet dietary protein hydrolysates, which may be derived from sturgeon muscle, have been reported to have versatile beneficial biological activities. Studying the biological activities of sturgeon muscle-derived hydrolysates holds much promise for adding value to sturgeon. The current study aimed to study the therapeutic anti-inflammatory effects of sturgeon muscle-derived hydrolysates and the underlying mechanisms. The administration of sturgeon hydrolysates (SH) significantly decreased the severity of DSS-induced damage, evidenced by increased body weight, colon length, and decreased disease activity index (DAI) and histological scores. SH also inhibited myeloperoxidase (MPO) activity and reduced the serum levels of IL-6, IL-1β, and TNF-α. Western blotting results revealed that SH suppressed DSS-induced activation of the NF-κB and MAPK pathways in the colon. Furthermore, SH partially restored the alteration of the gut microbiota in colitic mice. SH increased the Bacteroidetes/Firmicutes ratio and the relative abundance of Ruminococcaceae, Porphyromonadaceae, and Bacteroidetes S24-7, while decreased the abundance of potentially harmful bacteria Erysipelotrichaceae and Enterococcaceae. These results suggest that SH inhibited DSS-induced colitis by regulating the NF-κB and MAPK pathways and modulating microbiota composition.

Characterization of the microbial community structure in intestinal segments of yak (Bos grunniens)

Yak (Bos grunniens), a ruminant, has a complex gastrointestinal microbial ecosystem, which is essential for host nutrition and health. However, not much is known about gut microbial communities of yak. This study was conducted to characterize the gut microbial diversity and composition of small intestinal and cecal contents of yaks through high-throughput sequencing targeting V3–V4 hypervariable region of 16S rRNA gene. A total of 916,934 high-quality sequences were obtained and 224 core operational taxonomic units (OTUs) shared all samples. The result showed that the microbial community in the small intestine was different from cecum sample. In all samples, the majority of bacterial phyla were Firmicutes, Bacteroidetes and Proteobacteria. A large proportion of anaerobes in the families Peptostreptococcaceae, Prevotellaceae, Flavobacteriaceae, Lachnospiraceae, and Succinivibrionaceae were present in the various intestinal segments. The relative abundance of Ruminococcaceae, Bacteroidaceae and Muribaculaceae were significantly higher in cecum than in other segments of intestines. At the genus level, Bacteroides was the most predominant genus in cecum. The results indicated that yak have abundant and diverse gut microbial community. In conclusion, this study characterized the profiles of microbial communities across intestinal segments and provide better insight into microbial population structure and diversity of yak.

Both gut microbiota and cytokines act to atherosclerosis in ApoE−/− mice

BackgroundSeveral studies have suggested a role for the gut microbiome and cytokines in atherosclerosis development, but combined analyses of the changes of the gut microbiota and cytokines have not been explored previously. MethodsWe treated ApoE−/− and wild-type mice with a high-fat diet for 12 weeks. The gut microbiome and cytokine composition were analyzed using 16S ribosomal DNA sequencing and RayBio Quantibody Arrays, respectively. GO and KEGG analysis were performed to rationalize the potential mechanisms involved in the process of atherosclerosis. ResultsGut bacterial characteristics in ApoE−/− mice were clearly separated and 21 gut bacterial clades were detected by the LEfSe analysis showing significant differences during the development of atherosclerosis. The relative abundance of Verrucomicrobia, Bacteroidaceae, Bacteroides, and Akkermansia showed significant positive correlations with serum total cholesterol, triglyceride (TG), high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Additionally, the relative abundance of Ruminococcaceae was positive with the level of HDL and the abundance of Rikenellaceae showed a negative relationship with the level of TG and LDL. Thirteen differentially expressed proteins were identified with P-value < 0.05. CXCL5, FGF2, and E-Selectin were significantly negatively associated with Akkermansia and Verrucomicrobia. Additionally, CXCL5 was significantly negatively correlated with Bacteroides and Bacteroidaceae. Three "cellular component" subcategories, 24 ″molecular function" subcategories, 752 ″biological process" subcategories and 29 statistically remarkable KEGG pathway categories were identified. ConclusionsGut microbiota changes of the mice having atherosclerosis and their relationship with the inflammatory status could be one of the major etiological mechanisms underlying atherosclerosis.

Dynamic Variations in Fecal Bacterial Community and Fermentation Profile of Holstein Steers in Response to Three Stepwise Density Diets.

Simple SummaryThe gastrointestinal microbial ecosystem of cattle impacts their health and productivity. Collection of fecal samples provides a non-invasive and practicable way to explore the relationships between fecal microbiota and host productivity or health. Fecal bacteria are influenced by diet, feeding regime, animal age, and health status. However, dynamic variations in the fecal fermentation profile and microbiota composition of finishing steers in response to variable diets are limited. In the current study, we conducted an 11-month tracking investigation to uncover the dynamic variations in fecal fermentation profile and bacterial community in steers fed three stepwise density diets. We found that fecal bacterial diversity decreased as dietary density increased and as the fattening phase continued. Our results revealed that fecal organic acids and bacterial composition were influenced by diet and fattening period. Our results also indicated that time-dependent variations of fecal fermentation profile and microbiota composition exist in the long-term fattening of steers in addition to diet stimulation. This study will be beneficial to reducing fecal contamination from the origin by optimizing diet and fattening time.The objective of this study was to track the dynamic variations in fecal bacterial composition and fermentation profile of finishing steers in response to three stepwise diets varied in energy and protein density. A total of 18 Holstein steers were divided into three groups in such a way that each group contained six animals and received one of three stepwise dietary treatments. Dietary treatments were C = standard energy and protein diet, H = high energy and protein diet, and L = low energy and protein diet. Animals were fattened for 11 months with a three-phase fattening strategy. Fecal samples were collected to evaluate the dynamics of fecal fermentation and bacterial composition in response to dietary treatments and fattening phases using 16S rRNA gene sequencing. Fecal acetate, propionate, and butyrate increased with increasing density of diet and as the fattening phase continued. The relative abundances of Firmicutes and Bacteroidetes dominated and showed 56.19% and 33.58%, respectively. Higher dietary density decreased the fecal bacterial diversity, Firmicutes to Bacteroidetes ratio, and the relative abundances of Ruminococcaceae_UCG-005, Rikenellaceae_RC9_gut_group, and Bacteroides, whereas higher dietary density increased the abundance of Prevotella_9. Our results indicated that both fecal fermentation profile and bacterial composition share a time-dependent variation in response to different dietary densities. This knowledge highlights that both diet and fattening phase impact fecal fermentation profile and bacterial composition, and may provide insight into strategies to reduce fecal contamination from the origin by optimizing diet and fattening time.

Gut microbiota analysis and its significance in vasovagal syncope in children.

Background:Vasovagal syncope (VVS) is common in children and greatly affect both physical and mental health. But the mechanisms have not been completely explained. This study was designed to analyze the gut microbiota in children with VVS and explore its clinical significance.Methods:Fecal samples from 20 VVS children and 20 matched controls were collected, and the microbiota were analyzed by 16S rRNA gene sequencing. The diversity and microbiota compositions of the VVS cases and controls were compared with the independent sample t test or Mann-Whitney U test. The correlation between the predominant bacteria and clinical symptoms was analyzed using Pearson or Spearman correlation test.Results:No significant differences in diversity were evident between VVS and controls (P > 0.05). At the family level, the relative abundance of Ruminococcaceae was significantly higher in VVS children than in controls (median [Q1, Q3]: 22.10% [16.89%, 27.36%] vs. 13.92% [10.31%, 20.18%], Z = −2.40, P < 0.05), and LEfSe analysis revealed Ruminococcaceae as a discriminative feature (linear discriminant analysis [LDA] score > 4, P < 0.05). The relative abundance of Ruminococcaceae in VVS patients was positively correlated with the frequency of syncope (r = 0.616, P < 0.01). In terms of its correlation with hemodynamics, we showed that relative abundance of Ruminococcaceae was negatively correlated with the systolic and diastolic pressure reduction at the positive response in head-up tilt test (HUTT; r = −0.489 and −0.448, all P < 0.05), but was positively correlated with the mean pressure drop and decline rate (r = 0.489 and 0.467, all P < 0.05) as well as diastolic pressure drop and decline rate at the HUTT positive response (r = 0.579 and 0.589, all P < 0.01) in VVS patients.Conclusion:Ruminococcaceae was the predominant gut bacteria and was associated with the clinical symptoms and hemodynamics of VVS, suggesting that gut microbiota might be involved in the development of VVS.

Individual variability of synaptic depression in the hippocampus of young male and female rats after neonatal pro-inflammatory stress

Several studies have suggested a role for the gut microbiome and cytokines in atherosclerosis development, but combined analyses of the changes of the gut microbiota and cytokines have not been explored previously.We treated ApoE−/− and wild-type mice with a high-fat diet for 12 weeks. The gut microbiome and cytokine composition were analyzed using 16S ribosomal DNA sequencing and RayBio Quantibody Arrays, respectively. GO and KEGG analysis were performed to rationalize the potential mechanisms involved in the process of atherosclerosis.Gut bacterial characteristics in ApoE−/− mice were clearly separated and 21 gut bacterial clades were detected by the LEfSe analysis showing significant differences during the development of atherosclerosis. The relative abundance of Verrucomicrobia, Bacteroidaceae, Bacteroides, and Akkermansia showed significant positive correlations with serum total cholesterol, triglyceride (TG), high-density lipoprotein (HDL) and low-density lipoprotein (LDL). Additionally, the relative abundance of Ruminococcaceae was positive with the level of HDL and the abundance of Rikenellaceae showed a negative relationship with the level of TG and LDL. Thirteen differentially expressed proteins were identified with P-value < 0.05. CXCL5, FGF2, and E-Selectin were significantly negatively associated with Akkermansia and Verrucomicrobia. Additionally, CXCL5 was significantly negatively correlated with Bacteroides and Bacteroidaceae. Three "cellular component" subcategories, 24 ″molecular function" subcategories, 752 ″biological process" subcategories and 29 statistically remarkable KEGG pathway categories were identified.Gut microbiota changes of the mice having atherosclerosis and their relationship with the inflammatory status could be one of the major etiological mechanisms underlying atherosclerosis.

Effects of pure plant secondary metabolites on methane production, rumen fermentation and rumen bacteria populations in vitro.

In this study, the effects of seven pure plant secondary metabolites (PSMs) on rumen fermentation, methane (CH4 ) production and rumen bacterial community composition were determined. Two in vitro trials were conducted. In trial 1, nine concentrations of 8-hydroxyquinoline, α-terpineol, camphor, bornyl acetate, α-pinene, thymoquinone and thymol were incubated on separate days using in vitro 24-hr batch incubations. All compounds tested demonstrated the ability to alter rumen fermentation parameters and decrease CH4 production. However, effective concentrations differed among individual PSMs. The lowest concentrations that reduced (p<.05) CH4 production were as follows: 8mg/L of 8-hydroxyquinoline, 120mg/L of thymoquinone, 240mg/L of thymol and 480mg/L of α-terpineol, camphor, bornyl acetate and α-pinene. These concentrations were selected for use in trial 2. In trial 2, PSMs were incubated in one run. Methane was decreased (p<.05) by all PSMs at selected concentrations. However, only 8-hydroxyquinoline, bornyl acetate and thymoquinone decreased (p<.05) CH4 relative to volatile fatty acids (VFAs). Based on denaturing gradient gel electrophoresis analysis, different PSMs changed the composition of bacterial communities to different extents. As revealed by Ion Torrent sequencing, the effects of PSMs on relative abundance were most pronounced in the predominant families, especially in Lachnospiraceae, Succinivibrionaceae, Prevotellaceae, unclassified Clostridiales and Ruminococcaceae. The CH4 production was correlated negatively (-.72; p<.05) with relative abundance of Succinivibrionaceae and positively with relative abundance of Ruminococcaceae (.86; p<.05). In summary, this study identified three pure PSMs (8hydroxyquinoline, bornyl acetate and thymoquinone) with potentially promising effects on rumen CH4 production. The PSMs tested in this study demonstrated considerable impact on rumen bacterial communities even at the lowest concentrations that decreased CH4 production. The findings from this study may help to elucidate how PSMs affect rumen bacterial fermentation.

Effects of bentonite Bgp35b-p on the gut microbiota of mice fed a high-fat diet.

Bentonite is a natural clay mineral with health-promoting effects due to its high adsorption abilities with high cation-exchange capacity. Previously, we found an anti-obesity effect for Bgp35b-p bentonite produced in South Korea, where its high adsorbent ability of dietary lipids possibly partially removed the lipidic environment in the gut (unpublished). It is hypothesized that Bgp35b-p affects the intestinal microbial community, and thus the microbial changes were investigated via next-generation sequencing targeting the bacterial 16S rRNA gene and bioinformatics using QIIME (Quantitative Insights Into Microbial Ecology) were performed on feces of C57BL/6 male mice fed a high-fat diet (HFD) with the Bgp35b-p. The HFD caused microbial dysbiosis, characterized by a decrease in the relative abundance of Bacteroidetes and an increase in abundance of Firmicutes and Proteobacteria. It was found that HFD + Bgp35b-p led to significant changes in the microbial compositions of family-level bacteria known as short-chain fatty-acid-producing bacteria. The relative abundance of Ruminococcaceae was significantly increased, and the abundances of Clostridiaceae and Lachnospiraceae were decreased by HFD + Bgp35b-p, shifting close to that in mice fed a normal diet. Bgp35b-p induced compositional changes in intestinal microbiota, which can be considered as a prebiotic effect, thus suggesting that bentonite may be a potential prebiotic functional supplement. © 2018 Society of Chemical Industry.

Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw

The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mLN CH4 gVS−1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.

Effects of bitter melon (Momordica charantia L.) on the gut microbiota in high fat diet and low dose streptozocin-induced rats

The effects on gut microbiota of type 2 diabetic rats fed a bitter melon formulation (BLSP, a lyophilized superfine powder) were investigated. BLSP treatment significantly reduced fasting blood glucose levels (p < 0.05) and serum insulin levels (p < 0.05) of the diabetic rats. The gut microbiota of treated and control rats were profiled by PCR amplification and pyrosequencing of 16S rRNA genes (V3–V9 region). BLSP significantly reduced the ratio of Firmicutes to Bacteroidetes in diabetic rats, while the relative abundances of Ruminococcaceae, Bacteroides and Ruminococcus were significantly lowered in BLSP-treated rats compared to diabetic rats. Additionally, BLSP significantly suppressed the activation of MAPK (JNK and p38). The results indicate that BLSP can significantly modify the proportions of particular gut microbiota in diabetic rats without disturbing the normal population diversity. By suppressing the activation of MAPK signaling pathway, a BLSP containing diet may ameliorate type 2 diabetes.

The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra).

For most mammals, including nonhuman primates, diet composition varies temporally in response to differences in food availability. Because diet influences gut microbiota composition, it is likely that the gut microbiota of wild mammals varies in response to seasonal changes in feeding patterns. Such variation may affect host digestive efficiency and, ultimately, host nutrition. In this study, we investigate the temporal variation in diet and gut microbiota composition and function in two groups (N = 13 individuals) of wild Mexican black howler monkeys (Alouatta pigra) over a 10-month period in Palenque National Park, Mexico. Temporal changes in the relative abundances of individual bacterial taxa were strongly correlated with changes in host diet. For example, the relative abundance of Ruminococcaceae was highest during periods when energy intake was lowest, and the relative abundance of Butyricicoccus was highest when young leaves and unripe fruit accounted for 68 % of the diet. Additionally, the howlers exhibited increased microbial production of energy during periods of reduced energy intake from food sources. Because we observed few changes in howler activity and ranging patterns during the course of our study, we propose that shifts in the composition and activity of the gut microbiota provided additional energy and nutrients to compensate for changes in diet. Energy and nutrient production by the gut microbiota appears to provide an effective buffer against seasonal fluctuations in energy and nutrient intake for these primates and is likely to have a similar function in other mammal species.

The microbiota regulates susceptibility to Fas-mediated acute hepatic injury

Whereas a significant role for intestinal microbiota in affecting the pathogenesis and progression of chronic hepatic diseases is well documented, the contribution of the intestinal flora to acute liver injury has not been extensively addressed. Elucidating the influence of the intestinal microbiota on acute liver inflammation would be important for better understanding the transition from acute injury to chronic liver disease. Using the Concanavalin A (ConA)-induced liver injury model in laboratory mice, we show that the severity of acute hepatic damage varies greatly among genetically identical mice raised in different environments and harboring distinct microbiota. Through reconstitution of germ-free (GF) mice, and the co-housing of conventional mice, we provide direct evidence that manipulation of the intestinal flora alters susceptibility to ConA-induced liver injury. Through deep sequencing of the fecal microbiome, we observe that the relative abundance of Ruminococcaceae, a Gram(+) family within the class Clostridia, but distinct from segmented filamentous bacteria, is positively associated with the degree of liver damage. Searching for the underlying mechanism(s) that regulate susceptibility to ConA, we provide evidence that the extent of liver injury following triggering of the death receptor Fas varies greatly as a function of the microbiota. We demonstrate that the extent of Fas-induced liver injury increases in GF mice after microbiota reconstitution, and decreases in conventionally raised mice following reduction in intestinal bacterial load, by antibiotic treatment. We also show that the regulation of sensitivity to Fas-induced liver injury is dependent upon the toll-like receptor signaling molecule MyD88. In conclusion, the status and composition of the intestinal microbiota determine the susceptibility to ConA-induced acute liver injury. The microbiota acts as a rheostat, actively modulating the extent of liver damage in response to Fas triggering.

Probiotic Dosing of Ruminococcus flavefaciens Affects Rumen Microbiome Structure and Function in Reindeer

Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.