16S Rdna Sequencing
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2021 ◽  
Vol 10 (1) ◽  
pp. 76
Julia Vincent ◽  
Béatrice Colin ◽  
Isabelle Lanneluc ◽  
René Sabot ◽  
Valérie Sopéna ◽  

Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.

2021 ◽  
Chen Tang ◽  
Xueqin Zhang ◽  
Jingxian Xie ◽  
Lingyu Zeng ◽  
Yuntian Xin ◽  

Abstract Background: Caesarean delivery (CD) is associated with newborns’ health risks due to the blocking of microbiome transfer. To understand the vertical bacterial seeding and reduce CD disadvantages, microbiome transmissions via anal and genital routes were investigated, and the efficiency of vaginal fluid swabbing treatment was evaluated using 16s rDNA sequencing-based techniques.Results: Pregnant women were recruited in the Women and Children’s Hospital, School of Medicine, Xiamen University from June 1st to August 15th, 2017. Maternal faeces (n = 26), maternal vaginal fluids (n = 26), and neonatal transitional stools (n = 26) were collected, while the participants underwent natural delivery (ND) (n = 6), CD (n = 4) and CD with vaginal fluid swabbing (CS) on their newborns (n = 16). 26 mothers with the median age 26.50 (25.00-27.25) years showed no substantial clinical differences. The newborns’ gut microbiota altered among ND, CD and CS, and clustered into two groups (PERMANOVA P < 0.01) of swabbing and no-swabbing exposure. Gut colonization of ND babies majorly originated from maternal vaginal microbes (PERMANOVA P = 0.08), no vertical transmission was observed via anal route in any group. The vaginal transfer partially occurred by swabbing, in which the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, Bacteroides, and Escherichia-Shigella in newborns were similar to their mothers. The recovered taxa predicted KEGG functions of biosynthesis, metabolism, and DNA replication and repair with benefits of low risks of digestive, cardiovascular, and immune diseases.Conclusions: The newborn’s gut microbiota is mainly shaped by maternal vaginal microbiota, and aberrant colonization initiated by CD is partly mitigated by the swabbing treatment.

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Zhenhua Wang ◽  
Zhaoling Cai ◽  
Markus W. Ferrari ◽  
Yilong Liu ◽  
Chengyi Li ◽  

Objective. Chronic heart failure (CHF) refers to a state of persistent heart failure that can be stable, deteriorated, or decompensated. The mechanism and pathogenesis of myocardial remodeling remain unknown. Based on 16S rDNA sequencing and metabolomics technology, this study analyzed the gut microbiota and serum metabolome in elderly patients with CHF to provide new insights into the microbiota and metabolic phenotypes of CHF. Methods. Blood and fecal samples were collected from 25 elderly patients with CHF and 25 healthy subjects. The expression of inflammatory factors in blood was detected by ELISA. 16S rDNA sequencing was used to analyze the changes in microorganisms in the samples. The changes of small molecular metabolites in serum samples were analyzed by LC-MS/MS. Spearman correlation coefficients were used to analyze the correlation between gut microbiota and serum metabolites. Results. Our results showed that the IL-6, IL-8, and TNF-α levels were significantly increased, and the IL-10 level was significantly decreased in the elderly patients with CHF compared with the healthy subjects. The diversity of the gut microbiota was decreased in the elderly patients with CHF. Moreover, Escherichia Shigella was negatively correlated with biocytin and RIBOFLAVIN. Haemophilus was negatively correlated with alpha-lactose, cellobiose, isomaltose, lactose, melibiose, sucrose, trehalose, and turanose. Klebsiella was positively correlated with bilirubin and ethylsalicylate. Klebsiella was negatively correlated with citramalate, hexanoylcarnitine, inosine, isovalerylcarnitine, methylmalonate, and riboflavin. Conclusion. The gut microbiota is simplified by the disease, and serum small-molecule metabolites evidently change in elderly patients with CHF. Serum and fecal biomarkers could be used for elderly patients with CHF screening.

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Yang Sun ◽  
Haotian Bai ◽  
Ji Qu ◽  
Jichao Liu ◽  
Jincheng Wang ◽  

Abstract Background Gas-producing perianal abscess raises the possibility of clostridial infection, with Clostridium perfringens being the most common causative agent, which is highly lethal if untreated timely. As the treatment of clostridial infections often differs from that of non-clostridial infections, which they may closely resemble, the importance of accurate pathogenic organism identification cannot be overemphasized. The 16S rDNA of bacteria is highly conserved within a species and among species of the same genus but demonstrates substantial variation between different species, thus making it a suitable genomic candidate for bacterial detection and identification. Case presentation Here, we report the case of a 53-year-old patient who was admitted to the hospital for a gas-producing perianal abscess. The patient was managed with ceftizoxime and ornidazole and then received debridement and drainage at the lesion on the second day after admission. The bacterial cultures of the patient isolates from the debridement showed a coinfection of Escherichia coli and Enterococcus faecium. Although perianal redness and swelling subsided obviously after the surgery, the patient was febrile to 38.3℃ with his left upper thigh red and swollen, aggravated with tenderness and crepitus. Considering insufficient debridement and the risk of incorrect identification of pathogens, a second debridement and drainage were performed 4 days after the primary operation, and 16S rDNA sequencing of the isolates implicated Clostridium perfringens infection. Given the discrepancies in diagnostic results and the treatment outcomes, Enterococcus faecium was identified as sample contamination, and a diagnosis of coinfection of Clostridium perfringens and Escherichia coli in gas-producing perianal abscess was confirmed. The patient was then successfully treated with meropenem and vancomycin and was discharged at 27 days of admission. Conclusions This case represents the first report of coinfection of both clostridial and non-clostridial organisms in gas-producing perianal abscess and the first case reporting the use of 16S rDNA sequencing in the diagnosis of perianal abscess. Timely pathogen identification is critical for treating gas-producing perianal abscess and an antibiotic regimen covering both aerobic and anaerobic organisms is recommended before true pathogens are identified.

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 407-407
Ki Beom Jang ◽  
Sung Woo Kim

Abstract This study aimed to evaluate supplemental effects of milk carbohydrates in whey permeate on jejunal mucosa-associated microbiota in nursery pigs during 7 to 11 kg BW. A total of 720 pigs at 7.5 kg BW were allotted to 6 treatments (6 pens/treatment and 20 pigs/pen). Treatments were 6 levels of whey permeate supplementation (0, 3.75, 7.50, 11.25, 15.00, and 18.75%) and fed to pigs for 11 d. On d 11, 36 pigs representing median BW of each pen were euthanized to collect the jejunal mucosa to evaluate microbiota in the jejunum by 16S rDNA sequencing. Data were analyzed using contrasts in MIXED procedure of SAS. Whey permeate contained 76.3% lactose and 0.4% milk oligosaccharides. Increasing whey permeate supplementation from 0 to 18.75% did not affect the alpha-diversity estimates of microbiota. Whey permeate supplementation tended to decrease (P = 0.073, 1.59 to 1.22) Firmicutes:Bacteroidetes compared with no addition of whey permeate. Increasing whey permeate supplementation tended to linearly increase Bifidobacteriaceae (P = 0.089, 0.73 to 1.11), decrease Enterobacteriaceae (P = 0.091, 1.04 to 0.52), decrease Stretococcaceae (P = 0.094, 1.50 to 0.71), and caused quadratic changes (P &lt; 0.05) on Lactobacillaceae (maximum: 9.14% at 12.91% whey permeate). Increasing whey permeate supplementation caused a quadratic change (P &lt; 0.05) on Lactobacillus_Salivarius (maximum: 0.92% at 7.35% whey permeate) and tended to cause quadratic changes on Lactobacillus_Rogosae (P = 0.083; maximum: 0.53% at 8.45% whey permeate) and Lactobacillus_Mucosae (P = 0.092; maximum: 0.70% at 6.98% whey permeate). In conclusion, supplementation of whey permeate as sources of lactose and milk oligosaccharides at a range from 7 to 13% seems to be beneficial to nursery pigs by increasing the abundance of lactic acid-producing bacteria in the jejunal mucosa.

Hui Shan Chua ◽  
Yih Harng Soh ◽  
Shih Keng Loong ◽  
Sazaly AbuBakar

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.

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Qi Zhang ◽  
Jing-Jing Guo ◽  
Yuen-Ming Yau ◽  
Ying-Jie Wang ◽  
Yan-Bin Cheng ◽  

Background. Stress ulcer (SU) is a serious gastrointestinal mucosal lesion under acute stress. Huanglian decoction is a famous traditional Chinese medicine prescription, which has been used to treat digestive system diseases for thousands of years. Many clinical cases have proved that Huanglian decoction has a good effect on SU. Some studies have shown that the intestinal bacteria will be changed accordingly when the gastrointestinal mucosa is damaged. However, there are few published reports on the effect of the intestinal microbiome with SU mice that were treated by Huanglian decoction. In this study, we investigated the effect of the fecal microbiome in mice with SU by the 16S rDNA sequencing technology. Methods. Male KM mice were induced by cold-restraint stress except for the normal control group and then treated by Huanglian decoction (Group HD) and Esomeprazole magnesium solution (Group ES) separately for 7 days. 16S rDNA sequencing technology analysis was applied to evaluate the changes of bacterial flora in mice feces. And, histopathological methods and molecular biological detection methods were also performed. Results. Huanglian decoction could help to repair the gastric mucosal injury and regulate the relative content of TNF-α and IL-1β. Moreover, Huanglian decoction could increase the relative abundance of intestinal probiotics in the intestine of mice with SU, especially in Verrucomicrobiae and Akkermansia. Conclusions. Huanglian decoction might effectively promote the repair of gastrointestinal mucosal injury and regulate the number and species of intestinal bacteria to maintain the stability of gastrointestinal microecology.

2021 ◽  
Vol 14 (1) ◽  
Vladislav Mokeev ◽  
Justin Flaven-Pouchon ◽  
Yiwen Wang ◽  
Nicole Gehring ◽  
Bernard Moussian

Abstract Objectives As in most organisms, the surface of the fruit fly Drosophila melanogaster is associated with bacteria. To examine whether this association depends on cuticle quality, we isolated and quantified surface bacteria in normal and melanized flies applying a new and simple protocol. Results On wild flies maintained in the laboratory, we identified two persistently culturable species as Lactobacillus plantarum and Acetobacter pomorum by 16S rDNA sequencing. For quantification, we showered single flies for DNA extraction avoiding the rectum to prevent contamination from the gut. In quantitative PCR analyses, we determined the relative abundance of these two species in surface wash samples. On average, we found 17-times more A. pomorum than L. plantarum. To tentatively study the importance of the cuticle for the interaction of the surface with these bacteria, applying Crispr/Cas9 gene editing in the initial wild flies, we generated flies mutant for the ebony gene needed for cuticle melanisation and determined the L. plantarum to A. pomorum ratio on these flies. We found that the ratio between the two bacterial species reversed on ebony flies. We hypothesize that the cuticle chemistry is crucial for surface bacteria composition. This finding may inspire future studies on cuticle-microbiome interactions.

2021 ◽  
Vol 12 ◽  
Yanjiao Li ◽  
Yitian Zang ◽  
Xianghui Zhao ◽  
Lin Liu ◽  
Qinghua Qiu ◽  

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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