16S Rrna
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2021 ◽  
Vol 12 ◽  
Zeiad Moussa ◽  
Doaa B. Darwish ◽  
Salma S. Alrdahe ◽  
WesamEldin I. A. Saber

The current study reported a new keratinolytic bacterium, which was characterized as Bacillus paramycoides and identified by 16S rRNA, and the sequence was then deposited in the GenBank (MW876249). The bacterium was able to degrade the insoluble chicken feather keratin (CFK) into amino acids (AA) through the keratinase system. The statistical optimization of the biodegradation process into AA was performed based on the Plackett–Burman design and rotatable central composite design (RCCD) on a simple solid-state fermentation medium. The optimum conditions were temperature, 37°C, 0.547 mg KH2PO4, 1.438 mg NH4Cl, and 11.61 days of incubation. Innovatively, the degradation of the CFK process was modeled using the artificial neural network (ANN), which was better than RCCD in modeling the biodegradation process. Differentiation of the AA by high-performance liquid chromatography (HPLC) revealed the presence of 14 AA including essential and non-essential ones; proline and aspartic acids were the most dominant. The toxicity test of AA on the HepG2 cell line did not show any negative effect either on the cell line or on the morphological alteration. B. paramycoides ZW-5 is a new eco-friendly tool for CFK degradation that could be optimized by ANN. However, additional nutritional trials are encouraged on animal models.

2021 ◽  
Vol 12 ◽  
Siyu Xu ◽  
Yang Liu ◽  
Jian Gao ◽  
Man Zhou ◽  
Jingyue Yang ◽  

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is one of the most prevalent pathogens causing bovine mastitis worldwide. However, there is a lack of comprehensive information regarding genetic diversity, complete profiles of virulence factors (VFs), and antimicrobial resistance (AMR) genes for SDSD associated with bovine mastitis in China. In this study, a total of 674 milk samples, including samples from 509 clinical and 165 subclinical mastitis cases, were collected from 17 herds in 7 provinces in China from November 2016 to June 2019. All SDSD isolates were included in phylogenetic analysis based on 16S rRNA and multi-locus sequence typing (MLST). In addition, whole genome sequencing was performed on 12 representative SDSD isolates to screen for VFs and AMR genes and to define pan-, core and accessory genomes. The prevalence of SDSD from mastitis milk samples was 7.57% (51/674). According to phylogenetic analysis based on 16S rRNA, 51 SDSD isolates were divided into 4 clusters, whereas based on MLST, 51 SDSD isolates were identified as 11 sequence types, including 6 registered STs and 5 novel STs (ST521, ST523, ST526, ST527, ST529) that belonged to 2 distinct clonal complexes (CCs) and 4 singletons. Based on WGS information, 108 VFs genes in 12 isolates were determined in 11 categories. In addition, 23 AMR genes were identified in 11 categories. Pan-, core and accessory genomes were composed of 2,663, 1,633 and 699 genes, respectively. These results provided a comprehensive profiles of SDSD virulence and resistance genes as well as phylogenetic relationships among mastitis associated SDSD in North China.

Biologia ◽  
2021 ◽  
Monika Drážovská ◽  
Marián Prokeš ◽  
Boris Vojtek ◽  
Jana Mojžišová ◽  
Anna Ondrejková ◽  

AbstractCoxiella burnetii is a worldwide zoonotic pathogen causing Q fever in various animal species and humans. In Slovakia, cases of C. burnetii infection in both animals and humans are confirmed every year. The role of horses in the epidemiology of this neglected disease is still unclear. In our study, we focused on a serosurvey of C. burnetii in the equine population in Slovakia by the ELISA method. Subsequently, a nested PCR was performed to detect the 16S rRNA fragment of the genus Coxiella. Among 184 horse sera, the presence of specific antibodies to C. burnetii was detected in four samples, representing a 2.17% seropositivity. All the positive horses were mares; two originated from Central Slovakia and two from Eastern Slovakia. Although the number of positive samples was too small for a determination of statistical significance, our results provide the first confirmation of antibodies to C. burnetii in horses from Slovakia. Although no positive PCR result was obtained, these serological findings may help to clarify the circulation of the pathogen in the environment.

Huibin Lu ◽  
Fei Liu ◽  
Tongchu Deng ◽  
Meiying Xu

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7WT, CY18WT, CY22WT, FT31WT, FT137WT, FT147WT, BYS50W, BYS107WT, LFS511WT, LX15WT, LX22WT and NL8WT) were isolated from streams in China. Comparisons based on 16S rRNA gene sequences indicated that these strains take species of genus Undibacterium as close neighbours. The reconstructed phylogenetic and phylogenomic trees also showed that these strains cluster with species of genus Undibacterium together. The genome G+C contents of these strains were in the range of 45.3 to 53.3 mol%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values among these strains and related strains were in the range of 70.4 to 94.1% and 19.3 to 55.3% except that the values between strains CY7WT and BYS50W were 99.0 and 91.8 %, respectively. Q-8 was their predominant respiratory quinone. C16 : 1  ω7c and C16 : 0 were their major fatty acids. Their polar lipids profiles were similar, including phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two kinds of unidentified aminolipids. Combining polyphasic taxonomic characteristics and phylogenetic relationships, twelve strains should represent eleven independent novel species of genus Undibacterium , for which the names Undibacterium baiyunense sp. nov. (type strain BYS107WT=GDMCC 1.2453T=KCTC 82653T), Undibacterium curvum sp. nov. (type strain CY22WT=GDMCC 1.1906T=KACC 21951T), Undibacterium fentianense sp. nov. (type strain FT137WT=GDMCC 1.2456T=KCTC 82656T), Undibacterium flavidum sp. nov. (type strain LX15WT=GDMCC 1.1910T=JCM 34286T), Undibacterium griseum sp. nov. (type strain FT31WT=GDMCC 1.1908T=KACC 21953T), Undibacterium hunanense sp. nov. (type strain CY18WT=GDMCC 1.1904T=KACC 21949T), Undibacterium luofuense sp. nov. (type strain LFS511WT=GDMCC 1.2458T=KCTC 82658T), Undibacterium nitidum sp. nov. (type strain LX22WT=GDMCC 1.1912T=KACC 21957T), Undibacterium rivi sp. nov. (type strain FT147WT=GDMCC 1.2457T=KCTC 82657T), Undibacterium rugosum sp. nov. (type strain CY7WT=GDMCC 1.1903T=KACC 21961T) and Undibacterium umbellatum sp. nov. (type strain NL8WT=GDMCC 1.1915T=KACC 21960T) are proposed.

2021 ◽  
Vol 21 (1) ◽  
Anirudha R. Dixit ◽  
Christina L. M. Khodadad ◽  
Mary E. Hummerick ◽  
Cory J. Spern ◽  
LaShelle E. Spencer ◽  

Abstract Background Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed sanitization on the plants’ microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. ‘Outredgeous’) and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli. Result E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. Conclusion Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

2021 ◽  
Héctor Rodriguez-Perez ◽  
Laura Ciuffreda ◽  
Carlos Flores

Abstract The study of microbial communities and their applications have been leveraged by the advances in sequencing techniques and bioinformatics tools. The Oxford Nanopore Technologies long read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays opening the possibility of its application outside specialized environments and real-time analysis of data. To complement the existing efficient library preparation protocol with a streamlined analytic workflow, here we present NanoRTax, a nextflow pipeline for nanopore 16S rRNA amplicon data that features state-of-art taxonomic classification tools and real-time capability. The pipeline is paired with a web-based visual interface to enable user-friendly inspections of the experiment in progress.

2021 ◽  
Vol 21 (1) ◽  
Dan Kim ◽  
Jun-Young Jung ◽  
Hyun-Seok Oh ◽  
Sam-Ryong Jee ◽  
Sung Jae Park ◽  

Abstract Background Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC. Methods This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing. Results The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively. Conclusion The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy. Trial registration: This trial was registered at http://cris.nih.go.kr. Registration No.: KCT0003352), Date: 2018–11-13.

Snædís H. Björnsdóttir ◽  
Sólveig K. Pétursdóttir ◽  
Elísabet E. Gudmundsdóttir ◽  
Edda Olgudóttir ◽  
Sigmar K. Stefansson ◽  

Red-pigmented strains of non-sporeforming, aerobic, chemoorganotrophic bacteria were isolated from intertidal hot springs in Laugarvík, NW-Iceland. Cells stained Gram-negative and formed pleomorphic rods that often had swollen ends and occurred singly or in filaments. Growth was observed at 40-65 °C (optimum at 60 °C), pH 6-9 (optimum at 6.5–8) and 0.5–5% (optimum at 1–2%) (w/v) NaCl. Strain ISCAR-4553T contained MK-7 as the main respiratory quinone and saturated iso and anteiso branched chains of 17 and 15 carbons as the main cellular fatty acids (83.4%). The G+C content of the DNA is 67.3 mol%. The highest 16S rRNA gene sequence similarity was with the genus Roseithermus (92.0%) and followed by Rhodothermus , Rubrivirga and Rubricoccus (88–90%). Genome and phenotype comparisons supported the affiliation of the novel isolates and the genus Roseithermus to the family Rhodothermaceae of the phylum Rhodothermaeota . The described isolates are proposed to be classified as representatives of a novel species belonging to a novel genus, with the name Rhodocaloribacter litoris gen. nov., sp. nov. The type strain is ISCAR-4553T (=DSM 110790T = ATCC TSD-179T).

Prakit Saingam ◽  
Doris Y. W. Di ◽  
Tao Yan

Abstract Hurricane-caused stormwater runoffs transport diverse terrestrial pollutants, adversely impact microbiological water quality, and introduce fecal and other pathogens to coastal water environments. This study investigated the genotypic diversity, phylogenetic composition, antibiotic resistance patterns, and virulence gene repertoire of the Enterococcus population in the Hilo Bay coastal water after the immediate impact of Hurricane Lane. DNA fingerprinting of Enterococcus isolates exhibited large genotypic diversity, while 16S rRNA gene sequencing identified four major species, including E. faecalis (34.7%), E. faecium (22.4%), E. hirae (22.4%), and E. durans (18.4%). Four common enterococcal virulence genes (cylA, esp, asa1, and gelE) were detected in the Enterococcus population, with significant portions of E. durans (33.3%), E. faecalis (41.2%), E. faecium (36.4%), and E. hirae (27.3%) isolates possessing two or more virulence genes. Considerable antibiotic resistance to rifampin, erythromycin, tetracycline, and nitrofurantoin was detected in the Enterococcus population, with one E. durans isolate showing vancomycin resistance. The results indicate considerable health implications associated with Enterococcus spp. in the hurricane-impacted tropical coastal water, illustrating the needs for more comprehensive understanding of the microbiological risks associated with storm-impacted coastal water.

Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.

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