scholarly journals Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen

2020 ◽  
Vol 8 (12) ◽  
pp. 2005
Author(s):  
Venkata Vinay Kumar Bandarupalli ◽  
Benoit St-Pierre
Keyword(s):  
De Novo ◽  
Production Systems ◽  
Rumen Fluid ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Bovine Rumen ◽  
Ruminal Acidosis ◽  
Rrna Gene Sequencing

The inclusion of starch-rich feedstuffs, a common practice in intensive ruminant livestock production systems, can result in ruminal acidosis, a condition that can severely impact animal performance and health. One of the main causes of acidosis is the rapid accumulation of ruminal short chain fatty acids (SCFAs) resulting from the microbial digestion of starch. A greater understanding of ruminal bacterial amylolytic activities is therefore critical to improving mitigation of acidosis. To this end, our manuscript reports the identification of a candidate starch utilizer (OTU SD_Bt-00010) using batch culturing of bovine rumen fluid supplemented with starch. Based on 16S rRNA gene sequencing and metagenomics analysis, SD_Bt-00010 is predicted to be a currently uncharacterized strain of Prevotella albensis. Annotation of de novo assembled contigs from metagenomic data not only identified sequences encoding for α-amylase enzymes, but also revealed the potential to metabolize xylan as an alternative substrate. Metagenomics also predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and further suggested that this candidate strain may be a lactate utilizer. Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial attributes for its ruminant host.

scholarly journals Live Bacillus subtilis natto Promotes Rumen Fermentation by Modulating Rumen Microbiota In Vitro

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1519
Author(s):  
Meinan Chang ◽  
Fengtao Ma ◽  
Jingya Wei ◽  
Junhao Liu ◽  
Xuemei Nan ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
Rumen Fluid ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rumen Fermentation ◽  
Rrna Gene ◽  
Bacillus Subtilis Natto ◽  
Rrna Gene Sequencing

Previous studies have shown that Bacillus subtilis natto affects rumen fermentation and rumen microbial community structure, which are limited to detect a few microbial abundances using traditional methods. However, the regulation of B. subtilis natto on rumen microorganisms and the mechanisms of microbiota that affect rumen fermentation is still unclear. This study explored the effects of live and autoclaved B. subtilis natto on ruminal microbial composition and diversity in vitro using 16S rRNA gene sequencing and the underlying mechanisms. Rumen fluid was collected, allocated to thirty-six bottles, and divided into three treatments: CTR, blank control group without B. subtilis natto; LBS, CTR with 109 cfu of live B. subtilis natto; and ABS, CTR with 109 cfu of autoclaved B. subtilis natto. The rumen fluid was collected after 0, 6, 12, and 24 h of fermentation, and pH, ammonia nitrogen (NH3-N), microbial protein (MCP), and volatile fatty acids (VFAs) were determined. The diversity and composition of rumen microbiota were assessed by 16S rRNA gene sequencing. The results revealed LBS affected the concentrations of NH3-N, MCP, and VFAs (p < 0.05), especially after 12 h, which might be attributed to changes in 18 genera. Whereas ABS only enhanced pH and NH3-N concentration compared with the CTR group (p < 0.05), which might be associated with changes in six genera. Supplementation with live B. subtilis natto improved ruminal NH3-N and propionate concentrations, indicating that live bacteria were better than autoclaved ones. This study advances our understanding of B. subtilis natto in promoting ruminal fermentation, providing a new perspective for the precise utilization of B. subtilis natto in dairy rations.

Rumen Microbiota Alterations During Ketosis is Associated with the Development of Mastitis in Dairy Cows

2021 ◽  
Author(s):  
Kaihe Xiang ◽  
Xiaoyu Hu ◽  
Ruiying Mu ◽  
Shuang Li ◽  
Ying Wang ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Rumen Fluid ◽  
Animal Husbandry ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Metabolism Disorder ◽  
Clinical Investigations ◽  
Rrna Gene Sequencing ◽  
Serious Disease

Abstract Backgroud: Mastitis is the most serious disease endangering animal husbandry, especially dairy farming. Clinical investigations indicated that cows suffering from ketosis have a higher probability of mastitis. Rumen microbiota is closely related to ruminant health. However, it is not clear what role it plays in this process.Results: The microbiota in rumen fluid and milk from ketosis cows were determined by 16S rRNA gene sequencing. The results showed that the richness of bacterial community both in rumen and milk were changed in ketosis cows. The abundance of genus Prevotella, Ruminococcus, Succinivibrionaceae_UCG-001 and Streptococcus in rumen fluid from ketosis cows decreased significantly and were negatively correlated with blood BHBA and milk SCC. In contrast, the abundance of genus Luteimonas, Thermomonas, Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, NK4A214_group, Paracoccus, Acetitomaculum, Prevotellaceae_UCG-003, Deinococcus, Saccharofermentans and Butyrivibrio in rumen fluid from ketosis cows increased significantly and were positively correlated with blood BHBA and milk SCC. In addition, the abundance of F082 and Thermomonas were increased, while the abundance of genus Acinetobacter and UCG-005 were reduced both in milk and rumen fluid in ketosis cows than healthy cows. Conclusions: Ketosis in dairy cows is capable of inducing mastitis. The rumen microbiota of ketotic cows changed significantly and is associated with the development of mastitis. Targeting rumen microbiota regulation may be a promising strategy to prevent metabolism disorder and its secondary diseases in dairy cows.

scholarly journals Isolation and Identification of Sodium Fluoroacetate Degrading Bacteria from Caprine Rumen in Brazil

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Expedito K. A. Camboim ◽  
Arthur P. Almeida ◽  
Michelle Z. Tadra-Sfeir ◽  
Felício G. Junior ◽  
Paulo P. Andrade ◽  
...  
Keyword(s):  
Rumen Fluid ◽  
16S Rrna Gene Sequencing ◽  
Positive Control ◽  
Control Measures ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Poisonous Plants ◽  
Degrading Bacteria ◽  
Rrna Gene Sequencing ◽  
Orbital Shaker

The objective of this paper was to report the isolation of two fluoroacetate degrading bacteria from the rumen of goats. The animals were adult goats, males, crossbred, with rumen fistula, fed with hay, and native pasture. The rumen fluid was obtained through the rumen fistula and immediately was inoculated 100 μL in mineral medium added with 20 mmol L−1sodium fluoroacetate (SF), incubated at 39°C in an orbital shaker.Pseudomonas fluorescens(strain DSM 8341) was used as positive control for fluoroacetate dehalogenase activity. Two isolates were identified by 16S rRNA gene sequencing asPigmentiphaga kullae(ECPB08) andAncylobacter dichloromethanicus(ECPB09). These bacteria degraded sodium fluoroacetate, releasing 20 mmol L−1of fluoride ion after 32 hours of incubation in Brunner medium containing 20 mmol L−1of SF. There are no previous reports of fluoroacetate dehalogenase activity forP. kullaeandA. dichloromethanicus. Control measures to prevent plant intoxication, including use of fences, herbicides, or other methods of eliminating poisonous plants, have been unsuccessful to avoid poisoning by fluoroacetate containing plants in Brazil. In this way,P. kullaeandA. dichloromethanicusmay be used to colonize the rumen of susceptible animals to avoid intoxication by fluoroacetate containing plants.

scholarly journals Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1727
Author(s):  
Viktoria Neubauer ◽  
Renee M. Petri ◽  
Elke Humer ◽  
Iris Kröger ◽  
Nicole Reisinger ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Dry Matter ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Dry Matter Intake ◽  
Rrna Gene ◽  
Ruminal Ph ◽  
Rumen Acidosis ◽  
Rrna Gene Sequencing ◽  
Fecal Ph

Starch-rich diets can cause subacute ruminal acidosis (SARA) in dairy cows with potentially different susceptibility according to lactation number. We wanted to evaluate the bacterial community and the fermentation end products in feces to study susceptibility to hindgut acidosis and dysbiosis. Sixteen dairy cows received a medium-concentrate diet (MC, 40% concentrate, 18.8% starch) for one week and a high-concentrate diet (HC, 60% concentrate, 27.7% starch, DM) for four weeks. Milk yield, dry-matter intake, chewing activity, ruminal pH, milk constituents, and fecal samples for short-chain fatty acids (SCFA), pH, and 16S rRNA-gene sequencing were investigated. The HC feeding caused a reduction in fecal pH, bacterial diversity and richness, an increase in total SCFA, and a separate phylogenetic clustering of MC and HC samples. Ruminal and fecal pH had fair correlation (r = 0.5). Cows in the second lactation (2ndL) had lower dry matter intake (DMI) than cows of third or fourth or more lactations (3rdL; ≥4 L), whereas DMI/kg body weight was lower for ≥4 L than for 2ndL and 3rdL cows. The mean ruminal pH was highest in ≥4 L, whereas the time spent below the SARA threshold was highest for 3rdL cows. The latter also had higher total SCFA in the feces. Our results suggest that hindgut dysbiosis is caused by increased substrate flow to the hindgut, but further investigations are needed to define hindgut acidosis. The 3rdL cows were most susceptible to rumen acidosis and hindgut dysbiosis due to high DMI level, but missing counter regulations, as suggested happening in 2ndL and ≥4 L cows.

scholarly journals The Nutritional Supplement L-Alpha Glycerylphosphorylcholine Promotes Atherosclerosis

2021 ◽  
Vol 22 (24) ◽  
pp. 13477
Author(s):  
Zeneng Wang ◽  
Jennie Hazen ◽  
Xun Jia ◽  
Elin Org ◽  
Yongzhong Zhao ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Nutritional Supplement ◽  
Mapk Signaling ◽  
Rrna Gene ◽  
Human Coronary Artery ◽  
Atherosclerosis Progression ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community ◽  
Mapk Signaling Pathways

L-alpha glycerylphosphorylcholine (GPC), a nutritional supplement, has been demonstrated to improve neurological function. However, a new study suggests that GPC supplementation increases incident stroke risk thus its potential adverse effects warrant further investigation. Here we show that GPC promotes atherosclerosis in hyperlipidemic Apoe−/− mice. GPC can be metabolized to trimethylamine N-oxide, a pro-atherogenic agent, suggesting a potential molecular mechanism underlying the observed atherosclerosis progression. GPC supplementation shifted the gut microbial community structure, characterized by increased abundance of Parabacteroides, Ruminococcus, and Bacteroides and decreased abundance of Akkermansia, Lactobacillus, and Roseburia, as determined by 16S rRNA gene sequencing. These data are consistent with a reduction in fecal and cecal short chain fatty acids in GPC-fed mice. Additionally, we found that GPC supplementation led to an increased relative abundance of choline trimethylamine lyase (cutC)-encoding bacteria via qPCR. Interrogation of host inflammatory signaling showed that GPC supplementation increased expression of the proinflammatory effectors CXCL13 and TIMP-1 and activated NF-κB and MAPK signaling pathways in human coronary artery endothelial cells. Finally, targeted and untargeted metabolomic analysis of murine plasma revealed additional metabolites associated with GPC supplementation and atherosclerosis. In summary, our results show GPC promotes atherosclerosis through multiple mechanisms and that caution should be applied when using GPC as a nutritional supplement.

scholarly journals Microbial Community and Short-Chain Fatty Acid Mapping in the Intestinal Tract of Quail

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1006 ◽  
Author(s):  
Xizhong Du ◽  
Yun Xiang ◽  
Fangfang Lou ◽  
Pingguang Tu ◽  
Xiaojun Zhang ◽  
...  
Keyword(s):  
Intestinal Tract ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Short Chain ◽  
Meat Production ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Population Sizes ◽  
Rrna Gene Sequencing ◽  
Almost All

Quail is raised throughout China for egg and meat production. To deeply understand the gastrointestinal microbial composition and metabolites of quail, the present study characterized the microbiota inhabiting five intestinal locations of eight-week-old quail using 16S rRNA gene sequencing and qPCR, and evaluated the concentrations of short-chain fatty acids (SCFAs) in each individual location using gas chromatography. The results showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Deferribacteres were the five most abundant phyla in the intestinal tract of quail. Firmicutes was largely dominant (>95%) in the small intestine, whereas Bacteroidetes increased significantly in the cecum (19.19%) and colorectum (8.09%). At the genus level, Lactobacillus was predominant in almost all sections (>50%) except in the cecum (7.26%), where Megamonas, Faecalibacterium, and Bacteroides were dominant. qPCR data indicated that the population sizes of both the total bacteria and proportions of the Firmicutes, Bacteroidetes, and Bacteroides group increased going from the proximal toward the distal end of the intestine in quail. The SCFA-producing bacterial genera Bacteroides, Faecalibacterium, Alistipes, Blautia, Parabacteroides, and Clostridium were of higher richness in the cecum and colorectum, where, accordingly, more SCFAs were produced. These findings will be helpful for the future study of quail microbiology, as well as its relationship with productive performance and health.

scholarly journals Bacillus asahii sp. nov., a novel bacterium isolated from soil with the ability to deodorize the bad smell generated from short-chain fatty acids

2004 ◽  
Vol 54 (6) ◽  
pp. 1997-2001 ◽  
Author(s):  
Isao Yumoto ◽  
Kikue Hirota ◽  
Shingo Yamaga ◽  
Yoshinobu Nodasaka ◽  
Tsuneshirou Kawasaki ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Fatty Acids Profile ◽  
Rrna Gene Sequencing ◽  
Chain Fatty Acids

In a screening campaign to isolate strains with the ability to remove the bad smell associated with animal faeces, strain MA001T was isolated from a soil sample obtained from Shizuoka prefecture, Japan. The isolate grew at pH 6–9 but not at pH 10. Cells were Gram-positive, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolate was positive for catalase and oxidase tests but negative for indole production, deamination of phenylalanine and H2S production. The isolate did not produce acid from any carbohydrates tested and could not grow in more than 2 % NaCl. The DNA G+C content was 39·4 mol%. The cellular fatty acids profile consisted of significant amount of C15 branched-chain fatty acids, iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain MA001T was closely related to Bacillus simplex and Bacillus psychrosaccharolyticus. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetically close neighbours (less than 9 %). On the basis of the phenotypic characteristics observed, phylogenetic data based on 16S rRNA gene sequencing and DNA–DNA relatedness data, it is concluded that the isolate should be classified as representing a novel species, for which the name Bacillus asahii is proposed. The type strain is MA001T (=JCM 12112T=NCIMB 13969T).

scholarly journals Potential Role of Probiotics in Ameliorating Psoriasis by Modulating Gut Microbiota in Imiquimod-Induced Psoriasis-Like Mice

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 2010
Author(s):  
Wenwei Lu ◽  
Yadan Deng ◽  
Zhifeng Fang ◽  
Qixiao Zhai ◽  
Shumao Cui ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Cytokines ◽  
Systemic Disease ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Strain Specificity ◽  
Bifidobacterium Adolescentis ◽  
Pathological Characteristics ◽  
Rrna Gene Sequencing

Psoriasis is an immune-mediated systemic disease that may be treated with probiotics. In this study, probiotic strains that could or could not decrease interleukin (IL)-17 levels were applied to imiquimod (IMQ)-induced psoriasis-like mice via oral administration. Bifidobacterium adolescentis CCFM667, B. breve CCFM1078, Lacticaseibacillus paracasei CCFM1074, and Limosilactobacillus reuteri CCFM1132 ameliorated psoriasis-like pathological characteristics and suppressed the release of IL-23/T helper cell 17 (Th17) axis-related inflammatory cytokines, whereas B. animalis CCFM1148, L. paracasei CCFM1147, and L. reuteri CCFM1040 neither alleviated the pathological characteristics nor reduced the levels of inflammatory cytokines. All effective strains increased the contents of short-chain fatty acids, which were negatively correlated with the levels of inflammatory cytokines. By performing 16S rRNA gene sequencing, the diversity of gut microbiota in psoriasis-like mice was found to decrease, but all effective strains made some specific changes to the composition of gut microbiota compared to the ineffective strains. Furthermore, except for B. breve CCFM1078, all other effective strains decreased the abundance of the family Rikenellaceae, which was positively correlated with psoriasis-like pathological characteristics and was negatively correlated with propionate levels. These findings demonstrated effects of strain-specificity, and how probiotics ameliorated psoriasis and provide new possibilities for the treatment of psoriasis.

scholarly journals SCFA producing bacteria shape the subtype of ADHD in children

2019 ◽  
Author(s):  
Chaonan Fan ◽  
Shijie Li ◽  
Rui Wang ◽  
Xiuqin Fan ◽  
Aiming Liang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Chromatographic Analysis ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Short Chain Fatty Acids ◽  
Population Based ◽  
Rrna Gene ◽  
Adhd Subtypes ◽  
Adhd Children ◽  
Rrna Gene Sequencing

Abstract There is little data on population-based identification of the gut microbiota with ADHD subtypes in children, yet whether the degree ADHD is characterized by short-chain fatty acids (SCFAs) remains unclear. We enrolled 59 ADHD children including 21 inattentive subtypes (ADHD-I), 20 combined subtypes (ADHD-C), 18 hyperactive-Impulsive subtypes (ADHD-H) and 23 healthy controls. The microbiota was characterized by 16S rRNA gene sequencing, and SCFA concentrations were determined by gas chromatographic analysis. Compared to the controls, we observed a decrease of 14 genera belonging to Ruminococcaceae, Lachnospiraceae, Verrucomicrobiaceae and Rikenellaceae family in ADHD-I, while Megamonas, Coprococcus_2 and Paraprevotella were significantly increased in ADHD-C. In addition, a lower abundance of Faecalibacterium, and a higher proportion of Marvinbryantia, Intestinimonas, Prevotella_9 and Eggerthella were detected in the ADHD-H. Analysis of fecal SCFAs showed that elevated levels of acetate and propionate were in ADHD subtypes. Furthermore, most of the bacterium associated with SCFAs overlapped with the differential bacterium in ADHD subtypes. Conclusion: Our data support the clinical distinction among different ADHD subtypes in children may also be reflected in alterations of specific gut microbiota, most of which are SCFA producing bacteria.

scholarly journals A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

2016 ◽  
Author(s):  
Matthew A Jackson ◽  
Jordana T Bell ◽  
Tim D Spector ◽  
Claire J Steves
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
De Novo ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Clustering Methods ◽  
Taxonomic Assignment ◽  
Biologically Relevant ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

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