scholarly journals Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features

mSystems ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Sander Wuyts ◽  
Stijn Wittouck ◽  
Ilke De Boeck ◽  
Camille N. Allonsius ◽  
Edoardo Pasolli ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Related Species ◽  
Lactobacillus Casei ◽  
Large Scale ◽  
Predictive Power ◽  
Upper Respiratory Tract ◽  
Closely Related Species ◽  
Species Type ◽  
Upper Respiratory ◽  
Surface Adhesins

ABSTRACT The closely related species of the Lactobacillus casei group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the L. casei species. We find that after reclassification, only 10 genomes remain classified as L. casei. These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an L. casei strain from the human upper respiratory tract and discovered that it and multiple other L. casei strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species as a potential probiotic organism. Although the genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a Lactobacillus strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains. This led to the identification of a catalase-encoding gene in all 10 L. casei sensu stricto strains, making it the first described catalase-positive species in the Lactobacillus genus. Moreover, we found that 6 of 10 L. casei genomes contained a SecA2/SecY2 gene cluster with two putative glycosylated surface adhesin proteins. Altogether, our results highlight current inconsistencies in the taxonomy of the L. casei group and reveal new clade-associated functional features. IMPORTANCE The closely related species of the Lactobacillus casei group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the L. casei species. We find that after reclassification, only 10 genomes remain classified as L. casei. These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an L. casei strain from the human upper respiratory tract and discovered that it and multiple other L. casei strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species as a potential probiotic organism.

ANALYSIS OF THE FREQUENCY OF ISOLATION OF CORYNEBACTERIA NON-DIPHTHERIA FROM PATIENTS WITH INFLAMMATORY DISEASES OF THE RESPIRATORY TRACT

2019 ◽  
Vol 64 (7) ◽  
pp. 430-434
Author(s):  
Galina G. Kharseeva ◽  
E. O. Mangutov ◽  
O. M. But ◽  
A. V. Chepusova ◽  
E. L. Alutina
Keyword(s):  
Respiratory Tract ◽  
Related Species ◽  
Inflammatory Diseases ◽  
Clinical Importance ◽  
Chronic Tonsillitis ◽  
Chronic Obstructive ◽  
Respiratory Pathogens ◽  
Upper Respiratory Tract ◽  
Closely Related Species ◽  
Chronic Obstructive Pulmonary Diseases

Corynebacteria non-diphtheria and, in particular, C. pseudodiphtheriticum species that are closely related to C. propinquum and C. striatum form a group of new respiratory pathogens leading to the development of bronchitis, tracheitis, exacerbation of chronic obstructive pulmonary diseases, nosocomial pneumonia and other pathology. The goal is to analyze the frequency of the release of Сorynebacteria non-diphtheria from the upper respiratory tract of patients with various inflammatory diseases of the respiratory tract. Strains of Сorynebacteria non-diphtheria (C. pseudodiphtheriticum, C. propinquum, C. accolens, et al.), isolated from patients with inflammatory diseases of the respiratory tract (60 pcs.) and practically healthy individuals (31 pcs.) were studied. Identification of Сorynebacteria was performed using the method of mass spectrometry (MALDI-ToFMS). Сorynebacteria non-diphtheria in the amount of 105 and higher were more frequently detected with the development of chronic tonsillitis (60.0%) and nasopharyngitis (30%). The strains of C. pseudodiphtheriticum (40.0±6.4%) and the closely related species C. propinquum (21.7±5.3%) were mainly found; much less often - C. accolens (8.3±3.6%), C. afermentans (6.7±3.3%), et al. In 86.7% of cases, Corynebacteria non-diphtheria were isolated from children. In chronic tonsillitis, C. pseudodiphtheriticum and the closely related species of C. propinquum were isolated more often; in nasopharyngitis and bronchitis - С. pseudodiphtheriticum. Isolation of Corynebacteria non-diphtheria and, especially, C. pseudodiphtheriticum, C. propinquum, C. accolens species from patients with inflammatory diseases of the respiratory tract in the amount of 105 and above, if there are no other pathogenic microorganisms in the role of microbial associates, of clinical importance.

scholarly journals Reduction of Influenza Virus Titer and Protection against Influenza Virus Infection in Infant Mice Fed Lactobacillus casei Shirota

2004 ◽  
Vol 11 (4) ◽  
pp. 675-679 ◽  
Author(s):  
Hisako Yasui ◽  
Junko Kiyoshima ◽  
Tetsuji Hori
Keyword(s):  
Influenza Virus ◽  
Respiratory Tract ◽  
Oral Administration ◽  
Lactobacillus Casei ◽  
Influenza Virus Infection ◽  
Interleukin 12 ◽  
Saline Control ◽  
Control Group ◽  
Upper Respiratory Tract ◽  
Upper Respiratory

ABSTRACT We investigated whether oral administration of Lactobacillus casei strain Shirota to neonatal and infant mice ameliorates influenza virus (IFV) infection in the upper respiratory tract and protects against influenza infection. In a model of upper respiratory IFV infection, the titer of virus in the nasal washings of infant mice administered L. casei Shirota (L. casei Shirota group) was significantly (P < 0.05) lower than that in infant mice administered saline (control group) (102.48 ± 100.31 and 102.78 ± 100.4, respectively). Further, the survival rate of the L. casei Shirota group was significantly (P < 0.05) higher than that of the control group (14.3 versus 40.0%). One day after infection, pulmonary NK cell activity and interleukin-12 production by mediastinal lymph node cells of mice in the L. casei Shirota group were significantly greater than those of mice in the control group. These findings suggest that oral administration of L. casei Shirota activates the immature immune system of neonatal and infant mice and protects against IFV infection. Therefore, oral administration of L. casei Shirota may accelerate the innate immune response of the respiratory tract and protect against various respiratory infections in neonates, infants, and children, a high risk group for viral and bacterial infections.

scholarly journals SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels.

2021 ◽  
Author(s):  
Heba H Mostafa ◽  
chun Huai Luo ◽  
C. Paul Morris ◽  
Maggie Li ◽  
Nicholas J Swanson ◽  
...  
Keyword(s):  
Cell Culture ◽  
Respiratory Tract ◽  
Large Scale ◽  
Infectious Virus ◽  
Time Frame ◽  
Molecular Testing ◽  
Upper Respiratory Tract ◽  
Symptomatic Infection ◽  
Viral Loads ◽  
Upper Respiratory

Abstract Introduction COVID-19 large scale immunization in the US has been associated with infrequent breakthrough positive molecular testing. Whether a positive test is associated with a high viral RNA load, specific viral variant, recovery of infectious virus, or symptomatic infection is largely not known. Methods In this study, we identified 133 SARS-CoV-2 positive patients who had received two doses of either Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273) vaccines, the 2nd of which was received between January and April of 2021. The positive samples were collected between January and May of 2021 with a time that extended from 2 to 100 days after the second dose. Samples were sequenced to characterize the whole genome and Spike protein changes and cycle thresholds that reflect viral loads were determined using a single molecular assay. Local SARS-CoV-2 IgG antibodies were examined using ELISA and specimens were grown on cell culture to assess the recovery of infectious virus as compared to a control unvaccinated cohort from a matched time frame. Results Of 133 specimens, 24 failed sequencing and yielded a negative or very low viral load on the repeat PCR. Of 109 specimens that were used for further genome analysis, 68 (62.4%) were from symptomatic infections, 11 (10.1%) were admitted for COVID-19, and 2 (1.8%) required ICU admission with no associated mortality. The predominant virus variant was the alpha (B.1.1.7), however a significant association between lineage B.1.526 and amino acid change S: E484K with positives after vaccination was noted when genomes were compared to a large control cohort from a matched time frame. A significant reduction of the recovery of infectious virus on cell culture as well as delayed time to the first appearance of cytopathic effect was accompanied by an increase in local IgG levels in respiratory samples of vaccinated individuals but upper respiratory tract IgG levels were not different between symptomatic or asymptomatic infections. Conclusions Vaccination reduces the recovery of infectious virus in breakthrough infections accompanied by an increase in upper respiratory tract local immune responses.

scholarly journals COVID19: an announced pandemic

2020 ◽  
Vol 11 (9) ◽  
Author(s):  
Sara Platto ◽  
Tongtong Xue ◽  
Ernesto Carafoli
Keyword(s):  
Respiratory Tract ◽  
Large Scale ◽  
Dilution Effect ◽  
Local Environment ◽  
Upper Respiratory Tract ◽  
Causative Locus ◽  
History Of ◽  
Chinese Province ◽  
Upper Respiratory ◽  
Entire World

Abstract A severe upper respiratory tract syndrome caused by the new coronavirus has now spread to the entire world as a highly contagious pandemic. The large scale explosion of the disease is conventionally traced back to January of this year in the Chinese province of Hubei, the wet markets of the principal city of Wuhan being assumed to have been the specific causative locus of the sudden explosion of the infection. A number of findings that are now coming to light show that this interpretation of the origin and history of the pandemic is overly simplified. A number of variants of the coronavirus would in principle have had the ability to initiate the pandemic well before January of this year. However, even if the COVID-19 had become, so to say, ready, conditions in the local environment would have had to prevail to induce the loss of the biodiversity’s “dilution effect” that kept the virus under control, favoring its spillover from its bat reservoir to the human target. In the absence of these appropriate conditions only abortive attempts to initiate the pandemic could possibly occur: a number of them did indeed occur in China, and probably elsewhere as well. These conditions were unfortunately present at the wet marked in Wuhan at the end of last year.

Numerical Simulation on Vortex Evolution in the Realistic Human Upper Respiratory Tract

2013 ◽  
Vol 446-447 ◽  
pp. 1621-1624
Author(s):  
Dong Sun ◽  
Zhi Hui Guo ◽  
Li Ming Tang ◽  
Guang Dong Wang ◽  
Xin Xi Xu
Keyword(s):  
Respiratory Tract ◽  
Large Scale ◽  
Ct Scanning ◽  
Anterior Wall ◽  
Vortex Structures ◽  
Small Scale ◽  
Upper Respiratory Tract ◽  
Eddy Simulation ◽  
Developed Turbulence ◽  
Upper Respiratory

The technology of CT scanning and 3D reconstruction were used to construct 3D model of realistic human upper respiratory tract, and the method of large eddy simulation was used to simulate the process of vortex evolution in the model subtly. The results show that, several vortex tubes with low vortex intensity are formed in the rear of mouth; transition occurred in the pharynx, and the vortex structures break up rapidly; fully developed turbulence appeared in trachea, and several vortexes the shapes of which are similar to the wall of trachea appeared on the anterior wall of trachea; the large-scale vortex breaks up the small-scale vortex structures gradually in the bronchi.

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