Coupling 16S rDNA Sequencing and Untargeted Mass Spectrometry for Milk Microbial Composition and Metabolites from Dairy Cows with Clinical and Subclinical Mastitis

Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to combine 16S rDNA sequencing and metaproteomics technologies to investigate the microbial composition and function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/day CrPyr. 16S rDNA sequencing revealed that there were no significant differences in the α-diversity indices between the two groups. By analyzing the level profiles of 700 distinct proteins, we found that the CrPyr administration increased the expression of enzymes involved in specific metabolic pathways including (i) fatty acid β-oxidation; (ii) interconversion from pyruvate to phosphoenolpyruvate, oxaloacetate, acetyl-CoA, and malate; (iii) glycolysis/gluconeogenesis and citrate cycle metabolism; and (iv) biosynthesis of amino acids. These results indicated that the increased generation of adenosine triphosphate during fatty acid β-oxidation or citrate cycle and the up-regulation synthesis of microbial protein in rumen of beef cattle treated with CrPyr may help decrease oxidative stress, regulate energy metabolism, and further improve the rumen fermentation characteristic under heat stress.

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Dietary Supplementation With Creatine Pyruvate Alter Rumen Microbiota Protein Function in Heat-Stressed Beef Cattle

10.21203/rs.3.rs-104570/v1 ◽

2020 ◽

Author(s):

Yanjiao Li ◽

Xianghui Zhao ◽

Lin Liu ◽

Kang Mao ◽

Mingren Qu ◽

...

Keyword(s):

Heat Stress ◽

Fatty Acid ◽

Beef Cattle ◽

16S Rdna ◽

Rumen Fermentation ◽

16S Rdna Sequencing ◽

Microbial Protein ◽

Microbial Composition ◽

Citrate Cycle ◽

Rdna Sequencing

Abstract Background: Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to combine 16S rDNA sequencing and metaproteomics technologies to investigate the microbial composition and function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/d CrPyr. Results: 16S rDNA sequencing revealed that there was no significant differences in the α-diversity indices between the two groups. By analyzing the expression profiles of 700 distinct proteins, we found that CrPyr administration increased the fatty acid β-oxidation, promoted the interconversion from pyruvate to phosphoenolpyruvate, acetyl-CoA and malate, up-regulated gluconeogenesis and citrate cycle metabolism, and promoted the biosynthesis of amino acids. Conclusions: The increased generation of ATP during fatty acid β-oxidation or citrate cycle and the up-regulation synthesis of microbial protein in rumen of beef cattle treated with CrPyr, may help decreased oxidative stress, regulate energy metabolism, and further improve the rumen fermentation characteristic under heat stress.

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MALDI-TOF Mass Spectrometry Fingerprinting Performance Versus 16S rDNA Sequencing to Identify Bacterial Microflora From Seafood Products and Sea Water Samples

Frontiers in Marine Science ◽

10.3389/fmars.2021.650116 ◽

2021 ◽

Vol 8 ◽

Author(s):

Thomas Brauge ◽

Sylvain Trigueros ◽

Arnaud Briet ◽

Sabine Debuiche ◽

Guylaine Leleu ◽

...

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Sea Water ◽

Species Level ◽

16S Rdna Sequencing ◽

Genus Level ◽

Maldi Tof ◽

Rdna Sequencing ◽

Seafood Products ◽

Tof Ms

We evaluated the performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) associated with the Bruker BioTyperTM V7.0.0 database for the identification of 713 bacterial strains isolated from seafood products and sea water samples (ANSES B3PA collection) under culture conditions that may have been significantly different from those used to create the reference spectrum vs. the 16S rDNA sequencing. We identified 78.8% of seafood isolates with 46.7% at the species level (Bruker score above 2) and 21.2% (Bruker score between 1.7 and 2) at the genus level by the two identification methods, except for 3.8% of isolates with a difference of identification between the two methods (Bruker score between 1.7 and 2). There were 41.9% isolates (Bruker score below 1.7) with the identification at the genus level. We identified 94.4% of seafood isolates with 16S rDNA sequencing. The MALDI-TOF allowed a better strain identification to the species level contrary to the 16s rDNA sequencing, which allowed an identification mainly to the genus level. MALDI-TOF MS in association with the Bruker database and 16S rDNA sequencing are powerful tools to identify a wide variety of bacteria from seafood but require further identification by biochemical, molecular technique or other conventional tests.

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Rapid Identification of Microorganisms Isolated from Pickled Vegetables by MALDI-TOF Mass Spectrometry

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.712-715.494 ◽

2013 ◽

Vol 712-715 ◽

pp. 494-497

Author(s):

Zhi Lei Tan ◽

Yu Qiao Wei ◽

Shuang Liang ◽

Ran Zhang ◽

Miao Liu ◽

...

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Leuconostoc Mesenteroides ◽

16S Rdna Sequencing ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Rdna Sequencing ◽

Pickled Vegetables ◽

Food Bacteria ◽

Tof Ms

Matrix-assisted laser desorption/ionization time-off light mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF MS identification of food bacteria was seldom reported. Ten strains isolated from different pickled vegetables were rapid identified by MALDI-TOF MS. The results of MALDI-TOF MS were confirmed by 16S rDNA sequencing method. Different score values in MALDI-TOF MS revealed nineLeuconostoc mesenteroides and oneStaphylococcus.Identification success at the species and genus levels was 90% (9/10) and 100% (10/10), respectively.16S rDNA sequencing results showed that nine stains were identified asLeuconostoc mesenteroides and one wasStaphylococcus saprophyticus.Results obtained demonstrate that MALDI-TOFMS is a promising method for discriminating and identifying food bacteria.

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Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin

Gut ◽

10.1136/gutjnl-2018-317200 ◽

2018 ◽

Vol 68 (2) ◽

pp. 289-300 ◽

Cited By ~ 59

Author(s):

Zhen He ◽

Raad Z Gharaibeh ◽

Rachel C Newsome ◽

Jllian L Pope ◽

Michael W Dougherty ◽

...

Keyword(s):

Dna Damage ◽

16S Rdna ◽

Clinical Isolate ◽

Campylobacter Jejuni ◽

Intestinal Inflammation ◽

Cytolethal Distending Toxin ◽

16S Rdna Sequencing ◽

Microbial Composition ◽

Rdna Sequencing ◽

The Impact

ObjectiveCampylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined.DesignGerm-free (GF) ApcMin/+mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis.ResultsGF ApcMin/+mice colonised with human clinical isolate C. jejuni81–176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni.ConclusionHuman clinical isolate C. jejuni 81–176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.

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Francisella philomiragia bacteremia in an immunocompromised patient: a rare case report

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-021-00475-2 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Hui Shan Chua ◽

Yih Harng Soh ◽

Shih Keng Loong ◽

Sazaly AbuBakar

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Acute Pulmonary Oedema ◽

Molecular Technique ◽

Type I ◽

16S Rdna Sequencing ◽

Maldi Tof Mass Spectrometry ◽

Prompt Treatment ◽

Maldi Tof ◽

Rdna Sequencing

Abstract Background Francisella philomiragia is a very rare opportunistic pathogen of humans which causes protean diseases such as pneumonia and other systemic infections. Subsequent failure of prompt treatment may result in poor prognosis with mortality among infected patients. Case presentation The present report describes a case of F. philomiragia bacteraemia first reported in Malaysia and Asian in a 60-year-old patient with underlying end-stage renal disease (ESRF) and diabetes mellitus. He presented with Acute Pulmonary Oedema with Non-ST-Elevation Myocardial Infarction (NSTEMI) in our hospital. He was intubated in view of persistent type I respiratory failure and persistent desaturation despite post haemodialysis. Blood investigation indicated the presence of ongoing infection and inflammation. The aerobic blood culture growth of F. philomiragia was identified using the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (Score value: 2.16) and confirmed by 16S Ribosomal DNA (16S rDNA) sequencing. He was discharged well on day 26 of admission, after completing one week of piperacillin/tazobactam and two weeks of doxycycline. Conclusion Clinical suspicion should be raised if patients with known risk factors are presenting with pneumonia or pulmonary nodules especially as these are the most common manifestations of F. philomiragia infection. Early diagnosis via accurate laboratory identification of the organism through MALDI-TOF mass spectrometry and molecular technique such as 16S rDNA sequencing are vital for prompt treatment that results in better outcomes for the afflicted patients.

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Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

Current Pharmaceutical Analysis ◽

10.2174/1573412916666200206160836 ◽

2020 ◽

Vol 16 ◽

Author(s):

Nidhi Srivastava ◽

Indira P. Sarethy

Keyword(s):

Ethyl Acetate ◽

16S Rdna ◽

Retention Index ◽

Ethyl Acetate Extract ◽

Similarity Index ◽

Antimicrobial Drug ◽

16S Rdna Sequencing ◽

Metabolite Fingerprinting ◽

Streptomyces Sp ◽

Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

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2-Way k-Means as a Model for Microbiome Samples

Journal of Healthcare Engineering ◽

10.1155/2017/5284145 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Weston J. Jackson ◽

Ipsita Agarwal ◽

Itsik Pe’er

Keyword(s):

Unsupervised Learning ◽

16S Rdna ◽

Mixture Model ◽

Vaginal Microbiome ◽

16S Rdna Sequencing ◽

Sequencing Data ◽

Cluster Assignment ◽

Rdna Sequencing

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

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