scholarly journals Effects of Land Transport Stress on Variations in Ruminal Microbe Diversity and Immune Functions in Different Breeds of Cattle

Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 599 ◽  
Author(s):  
Li ◽  
Shah ◽  
Wang ◽  
Peng ◽  
Hu ◽  
...  
Keyword(s):  
Volatile Fatty Acids ◽  
High Throughput Sequencing ◽  
Immune Functions ◽  
Microbial Composition ◽  
Yellow Cattle ◽  
Tnf Α ◽  
Ruminal Microbiota ◽  
Transport Stress ◽  
Beef Cattle Production ◽  
Microbe Diversity

The intensity and specialization of beef cattle production make off-site fattening, and introduce new breeds need transportation to achieve the goals. The present study was aimed to investigate effects of land transport stress on hormones levels, microbial fermentation, microbial composition, immunity and correlation among them among Simmental Crossbred Cattle (SC), Native Yellow Cattle (NY), and Cattle Yak (CY). High-throughput sequencing was used to investigate the rumen microbial diversity. After transport stress cortisol (COR), adrenocorticotropic hormone (ACTH) and pro-inflammatory cytokines IL-6, TNF-α, and IL-1β were increased (p < 0.05) in all groups. Rumen lipopolysaccharide (LPS) was increased (p < 0.05) in SC and CY groups. Total volatile fatty acids were increased (p < 0.05) in all groups. The ruminal microbiota about OTUs, Chao1, and Shannon in SC and CY groups were higher than before transport. Prevotella1 in NY group was higher (p < 0.05) than other groups before transport; after transport Firmicutes and Lactobacillus were increased (p < 0.05) than other groups in CY. Lactobacillus was positively correlated with IL-6 and IL-4. Under transport stress, cattle may suffer from inflammatory response through modulating HPA axis and microbiota metabolite affects the secretion of hormone levels and immune function and breeds factor affect the performance of stress resistance.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Timothy P. Jenkins ◽  
David I. Pritchard ◽  
Radu Tanasescu ◽  
Gary Telford ◽  
Marina Papaiakovou ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Experimental Infection ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Placebo Treatment ◽  
Sequencing Data ◽  
Faecal Microbiota ◽  
Microbial Composition ◽  
Necator Americanus ◽  
Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

scholarly journals Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1492 ◽  
Author(s):  
Ben J. Callahan ◽  
Kris Sankaran ◽  
Julia A. Fukuyama ◽  
Paul J. McMurdie ◽  
Susan P. Holmes
Keyword(s):  
High Throughput Sequencing ◽  
Linear Models ◽  
Reference Database ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Nonparametric Testing ◽  
Abundance Estimates ◽  
Taxonomic Markers ◽  
Microbiome Data ◽  
Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

scholarly journals Oxidative Stress in Dairy Cows: Insights into the Mechanistic Mode of Actions and Mitigating Strategies

Antioxidants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1918
Author(s):  
Aurele Gnetegha Ayemele ◽  
Mekonnen Tilahun ◽  
Sun Lingling ◽  
Samy Abdelaziz Elsaadawy ◽  
Zitai Guo ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Volatile Fatty Acids ◽  
Molecular Mechanisms ◽  
Body Condition Score ◽  
Animal Health ◽  
Protein Carbonyl ◽  
Feed Additives ◽  
High Density Lipoproteins ◽  
Immune Functions ◽  
Antioxidant Genes

This review examines several molecular mechanisms underpinning oxidative stress in ruminants and their effects on blood and milk oxidative traits. We also investigate strategies to alleviate or repair oxidative damages by improving animal immune functions using novel feed additives. Microbial pathogenic cells, feeding management, and body condition score were some of the studied factors, inducing oxidative stress in ruminants. The predominance of Streptococcus spp. (24.22%), Acinetobacter spp. (21.37%), Romboutsia spp. (4.99%), Turicibacter spp., (2.64%), Stenotrophomonas spp. (2.33%), and Enterococcus spp. (1.86%) was found in the microbiome of mastitis cows with a decrease of d-mannose and increase of xanthine:guanine ratio when Streptococcus increased. Diversity of energy sources favoring the growth of Fusobacterium make it a keystone taxon contributing to metritis. Ruminal volatile fatty acids rose with high-concentrate diets that decreased the ruminal pH, causing a lysis of rumen microbes and release of endotoxins. Moreover, lipopolysaccharide (LPS) concentration, malondialdehyde (MDA), and superoxide dismutase (SOD) activities increased in high concentrate cows accompanied by a reduction of total antioxidant capacity (T-AOC), glutathione peroxidase (GPx), and catalase (CAT) activity. In addition, albumin and paraoxonase concentrations were inversely related to oxidative stress and contributed to the protection of low-density and high-density lipoproteins against lipid peroxidation, protein carbonyl, and lactoperoxidase. High concentrate diets increased the expression of MAPK pro-inflammatory genes and decreased the expression of antioxidant genes and proteins in mammary epithelial tissues. The expression levels of NrF2, NQO1, MT1E, UGT1A1, MGST3, and MT1A were downregulated, whereas NF-kB was upregulated with a high-grain or high concentrate diet. Amino-acids, vitamins, trace elements, and plant extracts have shown promising results through enhancing immune functions and repairing damaged cells exposed to oxidative stress. Further studies comparing the long-term effect of synthetic feed additives and natural plant additives on animal health and physiology remain to be investigated.

scholarly journals Effects of sulfonamide antibiotics on digestion performance and microbial community during swine manure anaerobic digestion

2020 ◽  
Vol 26 (1) ◽  
Author(s):  
Shaona Wang ◽  
Kang Du ◽  
Rongfang Yuan ◽  
Huilun Chen ◽  
Fei Wang ◽  
...  
Keyword(s):  
Organic Matter ◽  
Anaerobic Digestion ◽  
Dissolved Organic Matter ◽  
Methane Production ◽  
Volatile Fatty Acids ◽  
High Throughput Sequencing ◽  
Batch Reactor ◽  
Inhibition Mechanism ◽  
Sulfonamide Antibiotics ◽  
High Concentration

The effects of four types of sulfonamide antibiotics (SAs), including sulfaquinoxaline, sulfamethoxazole, sulfamethoxydiazine and sulfathiazole, on the digestion performance during anaerobic digestion process were studied using a lab-scale anaerobic sequencing batch reactor, and the changes of the community structure in the presence of SAs were investigated with the help of high throughput sequencing. The results indicated that when SAs were added, the hydrolytic acidification process was inhibited, and the accumulation of volatile fatty acids (VFAs) was induced, resulting in the suppression of methane production. However, the inhibition mechanism of different SAs was quite different. The inhibitory effect of high concentration of SAs on the hydrolysis of solid particulate matter into dissolved organic matter followed the order of sulfaquinoxaline > sulfamethoxydiazine > sulfathiazole > sulfamethoxazole. SAs have obvious inhibitory effects on acidification and methanation of dissolved organic matter, especially sulfathiazole. The richness and the community composition of the microorganism including bacteria and archaea in the digestion system were affected by SAs. Under the effect of SAs, the relative abundance of many microorganisms is negatively correlated with methane production, among which Methanobrevibacter, a kind of Archaea, had the greatest influence on methane production.

scholarly journals Microbial Structure and Energy Generation in Microbial Fuel Cells Powered with Waste Anaerobic Digestate

Energies ◽  
2020 ◽  
Vol 13 (18) ◽  
pp. 4712
Author(s):  
Dawid Nosek ◽  
Agnieszka Cydzik-Kwiatkowska
Keyword(s):  
Fuel Cells ◽  
Microbial Fuel Cells ◽  
Volatile Fatty Acids ◽  
Current Knowledge ◽  
Oxygen Demand ◽  
Electricity Production ◽  
Stable Operation ◽  
Microbial Structure ◽  
Microbial Composition ◽  
Start Up

Development of economical and environment-friendly Microbial Fuel Cells (MFCs) technology should be associated with waste management. However, current knowledge regarding microbiological bases of electricity production from complex waste substrates is insufficient. In the following study, microbial composition and electricity generation were investigated in MFCs powered with waste volatile fatty acids (VFAs) from anaerobic digestion of primary sludge. Two anode sizes were tested, resulting in organic loading rates (OLRs) of 69.12 and 36.21 mg chemical oxygen demand (COD)/(g MLSS∙d) in MFC1 and MFC2, respectively. Time of MFC operation affected the microbial structure and the use of waste VFAs promoted microbial diversity. High abundance of Deftia sp. and Methanobacterium sp. characterized start-up period in MFCs. During stable operation, higher OLR in MFC1 favored growth of exoelectrogens from Rhodopseudomonas sp. (13.2%) resulting in a higher and more stable electricity production in comparison with MFC2. At a lower OLR in MFC2, the percentage of exoelectrogens in biomass decreased, while the abundance of genera Leucobacter, Frigoribacterium and Phenylobacterium increased. In turn, this efficiently decomposed complex organic substances, favoring high and stable COD removal (over 85%). Independent of the anode size, Clostridium sp. and exoelectrogens belonging to genera Desulfobulbus and Acinetobacter were abundant in MFCs powered with waste VFAs.

scholarly journals Bioregional Alterations in Gut Microbiome Contribute to the Plasma Metabolomic Changes in Pigs Fed with Inulin

2020 ◽  
Vol 8 (1) ◽  
pp. 111 ◽  
Author(s):  
Weida Wu ◽  
Li Zhang ◽  
Bing Xia ◽  
Shanlong Tang ◽  
Lei Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Mantel Test ◽  
Plasma Metabolites ◽  
Microbial Composition ◽  
Regional Effects ◽  
Host Interaction ◽  
Β Diversity ◽  
Branched Chain ◽  
Host Metabolism

Inulin (INU) is a non-digestible carbohydrate, known for its beneficial properties in metabolic disorders. However, whether and how gut microbiota in its regulation contributes to host metabolism has yet to be investigated. We conduct this study to examine the possible associations between the gut microbiota and circulating gut microbiota–host co-metabolites induced by inulin interventions. Plasma and intestinal site samples were collected from the pigs that have consumed inulin diet for 60 days. High-throughput sequencing was adopted for microbial composition, and the GC-TOF-MS-based metabolomics were used to characterize featured plasma metabolites upon inulin intervention. Integrated multi-omics analyses were carried out to establish microbiota–host interaction. Inulin consumption decreased the total cholesterol (p = 0.04) and glucose (p = 0.03) level in serum. Greater β-diversity was observed in the cecum and colon of inulin-fed versus that of control-fed pigs (p < 0.05). No differences were observed in the ileum. In the cecum, 18 genera were altered by inulin, followed by 17 in the colon and 6 in the ileum. Inulin increased propionate, and isobutyrate concentrations but decreased the ratio of acetate to propionate in the cecum, and increased total short fatty acids, valerate, and isobutyrate concentrations in the colon. Metabolomic analysis reveals that indole-3-propionic acid (IPA) was significantly higher, and the branched-chain amino acids (BCAA), L-valine, L-isoleucine, and L-leucine are significantly lower in the inulin groups. Mantel test and integrative analysis revealed associations between plasma metabolites (e.g., IPA, BCAA, L-tryptophan) and inulin-responsive cecal microbial genera. These results indicate that the inulin has regional effects on the intestine microbiome in pigs, with the most pronounced effects occurring in the cecum. Moreover, cecum microbiota plays a pivotal role in the modulation of circulating host metabolites upon inulin intervention

scholarly journals Acorus gramineusand and Euodia ruticarpa Steam Distilled Essential Oils Exert Anti-Inflammatory Effects Through Decreasing Th1/Th2 and Pro-/Anti-Inflammatory Cytokine Secretion Ratios In Vitro

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 338 ◽  
Author(s):  
Tzu-He Yeh ◽  
Jin-Yuarn Lin
Keyword(s):  
Essential Oils ◽  
Immune Cells ◽  
Cytokine Secretion ◽  
Enzyme Linked Immunosorbent Assay ◽  
Total Flavonoids ◽  
Immune Functions ◽  
Immune Balance ◽  
Tnf Α ◽  
Th2 Polarization ◽  
Anti Inflammatory

To clarify the effects of steam distilled essential oils (SDEO) from herbs used in traditional Chinese medicine on immune functions, two potential herbs, Acorus gramineusand (AG) and Euodia ruticarpa (ER) cultivated in Taiwan, were selected to assess their immunomodulatory effects using mouse primary splenocytes and peritoneal macrophages. T helper type 1 lymphocytes (Th1) (IL-2), Th2 (IL-5), pro-inflammatory (TNF-α) and anti-inflammatory (IL-10) cytokines secreted by correspondent immune cells treated with SDEO samples were determined using enzyme-linked immunosorbent assay. The total amounts of potential phytochemicals, including total flavonoids, polyphenols and saponins, in these two selected SDEOs were measured and correlated with cytokine levels secreted by immune cells. Our results evidenced that ER SDEO is rich in total flavonoids, polyphenols and saponins. Treatments with AG and ER SDEO significantly (p < 0.05) increased IL-5/IL-2 (Th2/Th1) cytokine secretion ratios by splenocytes, suggesting that both AG and ER SDEO have the Th2-polarization property and anti-inflammatory potential. In addition, AG and ER SDEO, particularly ER SDEO, markedly decreased TNF-α/IL-10 secretion ratios by macrophages in the absence or presence of lipopolysaccharide (LPS), exhibiting substantial effects on spontaneous and LPS-induced inflammation. Significant correlations were found between the total polyphenols, flavonoids or saponins content in the two selected SDEOs and Th1/Th2 immune balance or anti-inflammatory ability in linear, non-linear or biphasic manners, respectively. In conclusion, our results suggest that AG and ER, particularly ER, SDEO have immunomodulatory potential in shifting the Th1/Th2 balance toward Th2 polarization in splenocytes and inhibiting inflammation in macrophages in the absence or presence of LPS.

Clinical characteristics associated with the properties of gut microbiota in peritoneal dialysis patients

2020 ◽  
pp. 089686082097698
Author(s):  
Na Jiang ◽  
Chenhong Zhang ◽  
Hao Feng ◽  
Jiangzi Yuan ◽  
Li Ding ◽  
...  
Keyword(s):  
Renal Function ◽  
Peritoneal Dialysis ◽  
Gut Microbiota ◽  
Clinical Characteristics ◽  
High Throughput Sequencing ◽  
Residual Renal Function ◽  
Microbial Composition ◽  
Cross Sectional ◽  
Dialysis Duration ◽  
Glucose Exposure

Background: Gut microbiota alters in patients with end-stage renal disease, which contributes to inflammation, atherosclerosis, and results in increased incidence of cardiovascular diseases. The present study investigated the potential clinical factors, which influence the gut microbial structure and function in patients undergoing peritoneal dialysis (PD). Methods: This is a cross-sectional study performed in 81 prevalent PD patients. Gut microbiota was assessed by high throughput sequencing of 16S ribosomal ribonucleic acid gene in fecal samples. Gas chromatography was conducted to measure stool short-chain fat acid (SCFA) concentrations. Demographic parameters and clinical characteristics, including dialysis regimen, residual renal function, nutrition, and inflammation, were retrieved and related to the properties of gut microbiota. Results: PD duration, peritoneal glucose exposure, and estimated glomerulus filtration rate (eGFR) were identified to be associated with microbial variations. Significant separation of microbial composition was shown between patients with short or long PD duration ( p = 0.015) and marginal differences were found between patients grouped by different levels of peritoneal glucose exposure ( p = 0.056) or residual renal function ( p = 0.063). A couple of gut bacteria showed different abundance at amplicon sequencing variant level between these patient groups ( p < 0.05). In addition, stool isobutyric and isovaleric acid concentrations were significantly reduced in patients with longer dialysis duration, higher peritoneal glucose exposure, or declined eGFR ( p < 0.05). Conclusions: This pilot study demonstrated that long dialysis duration, high peritoneal glucose exposure, and loss of residual renal function were associated with gut microbiota alteration and reduced branched-chain SCFA production in PD patients.

scholarly journals Intestinal epithelial cell-specific IGF1 promotes the expansion of intestinal stem cells during epithelial regeneration and functions on the intestinal immune homeostasis

2018 ◽  
Vol 315 (4) ◽  
pp. E638-E649 ◽  
Author(s):  
Yu Zheng ◽  
Yongli Song ◽  
Qi Han ◽  
Wenjie Liu ◽  
Jiuzhi Xu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Epithelial Cell ◽  
Intestinal Epithelial Cell ◽  
High Throughput Sequencing ◽  
Secretory Cells ◽  
Intestinal Epithelial ◽  
Epithelial Stem Cells ◽  
Microbial Composition ◽  
Epithelial Regeneration

It is well known that insulin-like growth factor 1 (IGF1) acts as a trophic factor in small intestine under both physiological and pathophysiological conditions. However, it still lacks direct in vivo evidence of the functions of intestinal epithelial cell (IEC)-specific IGF1 under both normal and pathological conditions. Using IEC-specific IGF1-knockout (cKO) mice and Lgr5-eGFP-CreERT mice, we demonstrate that IEC-specific IGF1 can enhance nutrient uptake, reduce protein catabolism and energy consumption, and promote the proliferation and expansion of intestinal epithelial cells, including intestinal epithelial stem cells and intestinal secretory cells. Next, we showed that IEC-specific IGF1 renders IECs resistant to irradiation and promotes epithelial regeneration. Strikingly, transcriptome profiling assay revealed that many differentially expressed genes involved in the differentiation and maturation of lymphoid lineages were significantly suppressed in the cKO mice as compared with the control mice. We demonstrated that deletion of IGF1 in IECs enhances bacterial translocation to the mesenteric lymph nodes and liver. Furthermore, high-throughput sequencing of 16S ribosomal RNA genes of gut microbiota revealed that IEC-specific IGF1 loss profoundly affected the gut microbial composition at various levels of classification. Therefore, our findings shed light on the in vivo roles of IEC-specific IGF1 in intestinal homeostasis, epithelial regeneration, and immunity, broadening our current insights on IGF1 functions.

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