Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease.

2021 ◽  
Vol 39 (3_suppl) ◽  
pp. 417-417
Author(s):  
Shyam K. Poudel ◽  
Roshan Padmanabhan ◽  
Kathryn Guinta ◽  
Tyler Stevens ◽  
Madhusudhan Sanaka ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cleveland Clinic ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Institutional Review ◽  
Sequencing Library ◽  
Acute And Chronic Pancreatitis ◽  
Bile Samples

417 Background: In pancreaticobiliary (PB) cancers, there is a paucity of data on predictive and pathophysiologic role of the biliary microbiome. We analyzed bile collected from patients with benign and malignant PB diseases to identify microbiomic signatures associated with malignancy. Methods: We collected bile samples from consenting patients during routine endoscopic retrograde cholangiopancreatography at the Cleveland Clinic, approved by the Institutional Review Board. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq and mixMC packages. Results: Of 46 enrolled patients, 32 had PB cancers including pancreatic (N = 25), cholangiocarcinoma (N = 6), and gallbladder (N = 1). The rest (N = 14) had benign PB diseases including acute and chronic pancreatitis, and gallstones. Using multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs), we found a predominance of genera Dicekeya (p = 0.0002), [ Eubacterium] hallii group (p = 0.0007) , Bacteroides (p = 0.00099) , Faecalibacterium (p = 0.007) , Facklamia (p = 0.013) , Peptococcus (p = 0.013) , Bergeyella (p = 0.0024) , Lachnospira (p = 0.026) , and Lactobacillus (p = 0.025) in bile samples from PB cancers as compared to benign PB diseases. Furthermore, bile samples from patients with pancreatic cancer showed an increased abundance of genera Enterobacter, Parabacteroides, Atopobium, Alloprevotella, Prevotella 7, Acinetobacter, Bergeyella, Clostridium sensu stricto, Lactobacillus, and Rothia; and a decreased abundance of genera Tannerella, Peptococcus, Colinsella, Capnocytophaga, Achromobacter, Ruminococcus 2, Bacteroides, Alistipes, Barnesiella,, Lachnoclostridium, Lautropia, Akkermansia, and Christensenellaceae R-7 group as compared to bile samples from patients with cholangiocarcinoma. Conclusions: Distinct microbiome signatures are associated with benign and malignant PB diseases. There is a difference in the relative abundance of OTUs in bile samples between patients with benign PB diseases vs PB cancers, and between pancreatic cancer vs cholangiocarcinoma. Our findings raise the possibility that either these OTUs have a role in carcinogenesis, or that changes in the microenvironment of benign PB diseases differ from PB cancers leading to distinct separation of the OTU clusters. Further studies to explore and validate our findings are needed.

Microbiome signature of bile from pancreatic and biliary tract cancer patients: A pilot study.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15744-e15744 ◽  
Author(s):  
Shyam K. Poudel ◽  
Roshan Padmanabhan ◽  
Prabhleen Chahal ◽  
Madhusudhan Sanaka ◽  
Tyler Stevens ◽  
...  
Keyword(s):  
Microbial Community ◽  
Biliary Tract ◽  
Cleveland Clinic ◽  
Microbial Community Analysis ◽  
Response To Treatment ◽  
Ductal Adenocarcinoma ◽  
Rrna Gene ◽  
Gallstone Pancreatitis ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing

e15744 Background: Recent studies especially in murine models have linked meta-organismal pathways in the gut microbial community to cancers of the pancreas and the biliary tract. However, data on microbiome in the biliary pool in patients to establish models for oncogenesis in the pancreatobiliary (PB) habitat have been limited. We analyzed bile collected from a pilot series of patients to identify microbiome signatures associated with malignancy. Methods: We collected bile samples from patients during routine endoscopic retrograde cholangiopancreatography in this study approved by the Cleveland Clinic Institutional Review Board for Human Subjects’ Protection. Of 10 patients, there were 5 with pancreatic ductal adenocarcinoma (PDA), 3 with cholangiocarcinoma (CC), 1 with ampullary adenocarcinoma, and 1 with gallstone pancreatitis. DNA was extracted from bile specimens using PowerViral RNA/DNA Isolation kit. Bacterial 16S rRNA gene amplification and library construction were performed according to the 16S Metagenomic Sequencing Library Preparation guide from Illumina. Post-sequencing analysis was done using QIIME (Quantitative Insights Into Microbial Ecology) and MICCA (MICrobial Community Analysis). Results: Most reads were from phyla Firmicutes (57.9%) and Proteobacteria (14.9%). One benign specimen (pancreatitis) separated clearly from the rest showing 98.9% of reads from Clostridium sensu stricto (phylum Firmicutes). Analysis of beta diversity showed six samples clustering tightly. Of these, 5 were PDA and 1 was CC. A second cluster included remaining 3 samples, 2 with CC and 1 with PDA; this latter had higher abundance of phyla Fusobacteria (90.6%) and Verrucomicrobia (92.9%). Conclusions: Select bacteria are differentially increased in malignant and benign PB diseases. Furthermore, distinct microbiome signatures may be associated with cancer in the pancreatic and biliary habitats. We intend to evaluate these findings in larger sample sizes and determine associations with clinical outcomes and response to treatment.

scholarly journals Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6316 ◽  
Author(s):  
Mikko J. Pyysalo ◽  
Pashupati P. Mishra ◽  
Kati Sundström ◽  
Terho Lehtimäki ◽  
Pekka J. Karhunen ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Intracranial Aneurysms ◽  
Gingival Crevicular Fluid ◽  
Tooth Brushing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Unruptured Intracranial Aneurysms ◽  
Neurosurgical Patients ◽  
Sequencing Library ◽  
Crevicular Fluid

ObjectivesThe objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms.MethodsGingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3–V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina’s 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2).ResultsBacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002;R2 = 34%;p(adjusted with age and sex) = 0.09;R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts.ConclusionsTooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients.

scholarly journals Bacterial community shift in nutrient-treated oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

2018 ◽  
Author(s):  
Thanachai Phetcharat ◽  
Pinan Dawkrajai ◽  
Thararat Chitov ◽  
Pisanu Wongpornchai ◽  
Schradh Saenton ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbial Enhanced Oil Recovery ◽  
Nutrient Treatment ◽  
Chemical Structures

AbstractMicrobial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, bacterial communities and the effects of elemental nutrient treatment of oil-bearing sandstone cores originated from six oil wells of an onshore reservoir was determined by tagged 16S rRNA gene amplicon sequencing, using Ion Torrent Metagenomic Sequencing Analysis. A total number of sequences were taxonomically classified into 43 phyla, 320 families, and 584 genera, with the dominant bacterial populations being related to Deinococcus-Thermus, and Betaproteobacteria. The nutrient treatment resulted in markedly increase in the relative abundance of Gammaproteobacteria. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera. To our knowledge, this is the first report on the effect of elemental nutrients on alteration of bacteria communities attached to the oil-bearing rock. It provides comprehensive data on bacterial, physical, and chemical structures within a reservoir and demonstrates how these parameters can be co-analyzed to serve as a basis for designing a MEOR process. It also provides a model of how a bacterial community in reservoirs’ strata can be altered by nutrient treatment to enhance the efficiency of MEOR applications.

scholarly journals Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort

2021 ◽  
Author(s):  
Hui Jiang ◽  
Shaoming Fang ◽  
Hui Yang ◽  
Congying Chen
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Gut Microbiome ◽  
Feed Efficiency ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
The Relationship

Abstract Feed efficiency is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism and fermentation of dietary indigestible components. Whether and which gut microbes affect feed efficiency in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 OTUs showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g. Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4 and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high feed efficiency), while 11 bacterial species including five Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had high abundance of the pathways related to amino acid metabolism and biosynthesis, but low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short chain fatty acids (SCFAs) were determined by UPLC-QTOF/MS and gas chromatograph, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving feed efficiency in pig production industry.

scholarly journals Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Clarisse Marotz ◽  
Kellen J. Cavagnero ◽  
Se Jin Song ◽  
Daniel McDonald ◽  
Stephen Wandro ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Room Temperature ◽  
Cost Effective ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Skin Microbiome ◽  
Metagenomic Sequencing ◽  
Sample Storage ◽  
Microbial Composition ◽  
Optimal Ratio

ABSTRACT As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 and performed shotgun metagenomic sequencing on remnant DNA from this experiment. Both results support the initial findings that 95% ethanol, a nontoxic, cost-effective preservative, is effective at preserving samples at room temperature for weeks. We expanded on this analysis by collecting a new set of fecal, saliva, and skin samples to determine the optimal ratio of 95% ethanol to sample. We identified optimal collection protocols for fecal samples (storing a fecal swab in 95% ethanol) and saliva samples (storing unstimulated saliva in 95% ethanol at a ratio of 1:2). Storing skin swabs in 95% ethanol reduced microbial biomass and disrupted community composition, highlighting the difficulties of low biomass sample preservation. The results from this study identify practical solutions for large-scale analyses of fecal and oral microbial communities. IMPORTANCE Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. Here, we validate findings that 95% ethanol efficiently preserves microbial composition at room temperature for weeks. We also identified the optimal ratio of 95% ethanol to sample for stool and saliva to preserve both microbial load and composition. These results provide rationale for an accessible, nontoxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples.

scholarly journals Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1825
Author(s):  
Mohamed Zeineldin ◽  
Ameer Megahed ◽  
Benjamin Blair ◽  
Brian Aldridge ◽  
James Lowe
Keyword(s):  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Post Intervention ◽  
Gastrointestinal Microbiome ◽  
Health And Wellbeing ◽  
Suckling Piglets ◽  
And Function ◽  
Changes Over Time ◽  
And Control ◽  
The Impact

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

scholarly journals Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiang Li ◽  
Yadan Huang ◽  
Shenglin Xin ◽  
Zhongyi Li
Keyword(s):  
Trophic Status ◽  
Alpha Diversity ◽  
Decisive Role ◽  
Sensu Stricto ◽  
Karst Area ◽  
Southwestern China ◽  
Rrna Gene ◽  
Karst Water ◽  
Bacterioplankton Community ◽  
Generation Sequencing

AbstractAlthough bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

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