scholarly journals Ribosome hibernation: a new molecular framework for targeting nonreplicating persisters of mycobacteria

Microbiology ◽  
2021 ◽  
Vol 167 (2) ◽  
Author(s):  
Yunlong Li ◽  
Manjuli R. Sharma ◽  
Ravi K. Koripella ◽  
Nilesh K. Banavali ◽  
Rajendra K. Agrawal ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Type Species ◽  
Drug Regimen ◽  
Content Type ◽  
Link Type ◽  
A Minor ◽  
Molecular Framework

Treatment of tuberculosis requires a multi-drug regimen administered for at least 6 months. The long-term chemotherapy is attributed in part to a minor subpopulation of nonreplicating Mycobacterium tuberculosis cells that exhibit phenotypic tolerance to antibiotics. The origins of these cells in infected hosts remain unclear. Here we discuss some recent evidence supporting the hypothesis that hibernation of ribosomes in M. tuberculosis, induced by zinc starvation, could be one of the primary mechanisms driving the development of nonreplicating persisters in hosts. We further analyse inconsistencies in previously reported studies to clarify the molecular principles underlying mycobacterial ribosome hibernation.

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Lina Sun ◽  
Wei Chen ◽  
Kaihua Huang ◽  
Weiguang Lyu ◽  
Xinhua Gao
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Pr China

Strain SJQ9T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9T fell within the genus Aquabacterium . The closest phylogenetic relatives of strain SJQ9T were Aquabacterium citratiphilum DSM 11900T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9T were consistent with those of the genus Aquabacterium : the major fatty acid was summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9T exhibited a DNA–DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900T and 28±3 % with A. commune DSM 11901T. Based on the obtained data, strain SJQ9T represents a novel species of the genus Aquabacterium , for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9T (=JCM 33106T=CCTCC AB 2018284T).

scholarly journals Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui
Keyword(s):  
Brown Alga ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
A Minor

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase

Microbiology ◽  
2021 ◽  
Vol 167 (9) ◽  
Author(s):  
Nirbhay Singh ◽  
Anu Chauhan ◽  
Ram Kumar ◽  
Sudheer Kumar Singh
Keyword(s):  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Type Species ◽  
Low Ph ◽  
Stress Conditions ◽  
Starvation Stress ◽  
Content Type ◽  
E Coli ◽  
Link Type

Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in Mycobacterium tuberculosis H37Rv (Mtb-Rv) and MRA_3031 in M. tuberculosis H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in Escherichia coli . Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing E. coli BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and E. coli IlvCs. The E. coli knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and E. coli IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of E. coli IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.

Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1083-1088 ◽  
Author(s):  
Kai Chen ◽  
Shu-Kun Tang ◽  
Guang-Li Wang ◽  
Guo-Xing Nie ◽  
Qin-Fen Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Bacterial strain 14-2AT, isolated from a long-term DDT-contaminated soil in China, was characterized by using a polyphasic approach to clarify its taxonomic position. Strain 14-2AT was found to be Gram-negative, aerobic, non-spore-forming, non-motile, non-flagellated and rod-shaped. The new isolate was able to grow at 4–42 °C, pH 6.0–9.0 and with 0–5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the family Sphingobacteriaceae . The 16S rRNA gene sequence of strain 14-2AT showed the highest similarity with Olivibacter oleidegradans TBF2/20.2T (99.4 %), followed by Pseudosphingobacterium domesticum DC-186T (93.8 %), Olivibacter ginsengisoli Gsoil 060T (93.6 %), Olivibacter terrae Jip13T (93.1 %), Olivibacter soli Gsoil 034T (92.8 %) and Olivibacter sitiensis AW-6T (89.6 %). The DNA–DNA hybridization value between strains 14-2AT and O. oleidegradans TBF2/20.2T was 34.45±2.11 %. Strain 14-2AT contained phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminophospholipid and phosphatidylinositol mannoside as the major polar lipids. The DNA G+C content was 41.2 mol%. MK-7 is the major isoprenoid quinone. Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH are the major fatty acids. The phenotypic and chemotaxonomic data confirmed the affiliation of strain 14-2AT to the genus Olivibacter . On the basis of the phylogenetic and phenotypic characteristics, and chemotaxonomic data, strain 14-2AT is considered to represent a novel species of the genus Olivibacter , for which the name Olivibacter jilunii sp. nov. is proposed; the type strain is 14-2AT ( = KCTC 23098T = CCTCC AB 2010105T).

scholarly journals Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis

Microbiology ◽  
2021 ◽  
Author(s):  
Céline Rens ◽  
Joseph D. Chao ◽  
Danielle L. Sexton ◽  
Elitza I. Tocheva ◽  
Yossef Av-Gay
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Type Species ◽  
Cell Envelope ◽  
Infectious Agent ◽  
Resistant Bacteria ◽  
Content Type ◽  
Link Type ◽  
Drug Resistant Bacteria ◽  
Macrophage Phagocytosis ◽  
Key Steps

The success of Mycobacterium tuberculosis as a pathogen is well established: tuberculosis is the leading cause of death by a single infectious agent worldwide. The threat of multi- and extensively drug-resistant bacteria has renewed global concerns about this pathogen and understanding its virulence strategies will be essential in the fight against tuberculosis. The current review will focus on phthiocerol dimycocerosates (PDIMs), a long-known and well-studied group of complex lipids found in the M. tuberculosis cell envelope. Numerous studies show a role for PDIMs in several key steps of M. tuberculosis pathogenesis, with recent studies highlighting its involvement in bacterial virulence, in association with the ESX-1 secretion system. Yet, the mechanisms by which PDIMs help M. tuberculosis to control macrophage phagocytosis, inhibit phagosome acidification and modulate host innate immunity, remain to be fully elucidated.

scholarly journals Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Isabelle Bernaquez ◽  
Christiane Gaudreau ◽  
Pierre A. Pilon ◽  
Sadjia Bekal
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Core Genome ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Interpretation Criteria

Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most Shigella spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91 Shigella flexneri and 232  Shigella sonnei isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related Shigella spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related S. sonnei outbreaks via wgMLST. The S. sonnei correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.

scholarly journals Construction and evaluation of a bioluminescent Pseudomonas aeruginosa reporter for use in preservative efficacy testing

Microbiology ◽  
2021 ◽  
Vol 167 (8) ◽  
Author(s):  
Laura Rushton ◽  
Denise Donoghue ◽  
Matthew Bull ◽  
Peter Jay ◽  
Eshwar Mahenthiralingam
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Type Species ◽  
Random Mutagenesis ◽  
Light Output ◽  
Rapid Decline ◽  
Content Type ◽  
Link Type ◽  
Term Evaluation ◽  
Positive Attribute

Preservative efficacy testing (PET) is a fundamental practice in industrial microbiology used to ensure product shelf-life and quality. To improve on current growth-based PET, bioluminescence was evaluated as a real-time bacterial viability indicator using Pseudomonas aeruginosa . Random mutagenesis of an industrial P. aeruginosa strain with a promoter-less luxCDABE mini-Tn5 was used to select a stable reporter (LUX12H5) with an un-altered growth and preservative susceptibility phenotype. Bioluminescence and viability were measured with and without preservatives (isothiazolinones, phenoxyethanol, and dimethyl dimethylol hydantoin) and an antibiotic comparator (ciprofloxacin). In the absence of antimicrobials, a good correlation between bioluminescence and viability (r2=0.92) was established. However, metabolic inhibition by isothiazolinone preservatives caused a rapid decline in light output that did not correlate to a reduced viability. Conversely, after ciprofloxacin exposure, the decline in viability was greater than that of bioluminescence. A positive attribute of the bioluminescence was the early detection of metabolic recovery and re-growth of preservative injured bacteria. Overall, while initial bioluminescence read-outs were less suited to current PET requirements, it shows promise as an early, direct indicator of bacterial regrowth in the context of long-term evaluation of preservative efficacy.

Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4181-4188 ◽  
Author(s):  
Andrei N. Shkoporov ◽  
Ekaterina V. Khokhlova ◽  
Andrei V. Chaplin ◽  
Lyudmila I. Kafarskaia ◽  
Alexei A. Nikolin ◽  
...  
Keyword(s):  
Type Species ◽  
Molar Ratio ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rich Media ◽  
Gene Sequence Analysis ◽  
The Family ◽  
A Minor ◽  
Acetic Acids

A novel obligately anaerobic, non-spore-forming, rod-shaped, non-motile Gram-reaction-negative bacterium was isolated from infant faeces. The strain, designated NSB1T, was able to grow on rich media at 30–37 °C, in the presence of up to 2 % (w/v) Oxgall and 2 % (w/v) NaCl. Cells of strain NSB1T produced catalase, but not urease and indole. Aesculin was not hydrolysed. The strain was able to utilize d-glucose, lactose, maltose, mannose and raffinose as electron donors. When grown on d-glucose, the main metabolic end products were propionic and acetic acids, with a minor product being succinic acid. The major cellular fatty acids, iso-C15 : 0 and anteiso-C15 : 0, were present at a 1 : 1 molar ratio. The major menaquinone was MK-11. The DNA G+C content was found to be 38.5 mol%. According to 16S rRNA gene sequence analysis strain NSB1T is a member of the family Porphyromonadaceae , phylum Bacteroidetes . The closest relatives of the strain were Barnesiella viscericola (88.2 % identity) and Barnesiella intestinihominis (87.4 % identity). On the basis of phenotypic and genotypic properties of strain NSB1T we conclude that this strain represent a novel species in a new genus within the family of Porphyromonadaceae for which the name Coprobacter fastidiosus gen. nov., sp. nov. is proposed. The type strain of the species is NSB1T ( = DSM 26242T, = VKM B-2743T).

Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Yeseul Shin ◽  
Jayoung Paek ◽  
Hongik Kim ◽  
Joong-Ki Kook ◽  
Young Hyo Chang
Keyword(s):  
Large Intestine ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Minor Amount ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Clostridium Symbiosum ◽  
A Minor

An obligately anaerobic, Gram-stain-negative, spore-forming, short rod-shaped bacterium, designated strain YH- T4B42T, was isolated from the large intestine of a mini-pig. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium aminophilum KCTC 5424T, Clostridium symbiosum KCTC 15329T and Clostridium butyricum KCTC 1871T, with 95.5, 92.4 and 83.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-T4B42T and the closest related strains were lower than 72 %. The G+C content of the isolate was 55.8 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1 cis 9, C14 : 0 and C18 : 0. The major end products of glucose fermentation were lactate, formate and acetate, with a minor amount of butyrate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, Clostridium vitabionis sp. nov., is proposed for strain YH-T4B42T (=KCTC 25105T=NBRC 114767T).

scholarly journals Cohnella nanjingensis sp. nov., an extracellular polysaccharide-producing bacterium isolated from soil

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3320-3324 ◽  
Author(s):  
Zhi Huang ◽  
Ya-jun Yu ◽  
Yuan-yuan Bao ◽  
Li Xia ◽  
Xia-fang Sheng ◽  
...  
Keyword(s):  
Type Species ◽  
Minor Component ◽  
Extracellular Polysaccharide ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
A Minor

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain D45T, was isolated from soil in Nanjing, China. The organism grew optimally at 30 °C, pH 7.0 and with 0 % NaCl (w/v). The 16S rRNA gene sequence of the isolate showed similarities lower than 97 % with respect to species of the genus Cohnella . The predominant respiratory quinone was MK-7, with MK-6 present as a minor component; anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The polar lipids of strain D45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, four phospholipids, two glycolipids, one aminolipid and two lipids. The DNA G+C content was 59.5 mol%. DNA–DNA hybridization of the isolate with two reference strains showed relatedness values of 33.4 % with Cohnella ginsengisoli DSM 18997T and 25.8 % with Cohnella thermotolerans DSM 17683T. The phylogenetic, chemotaxonomic and phenotypic data supported the classification of strain D45T as a representative of a novel species of the genus Cohnella , for which the name Cohnella nanjingensis sp. nov. is proposed. The type strain is D45T ( = CCTCC AB 2014067T = DSM 28246T).

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