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Frontiers in Microbiology 2019Deciphering the evolutionary history of pathogenic bacteria and their near neighbors may help to understand the genetic or ecological bases which led to their pathogenic...
Deciphering the evolutionary history of pathogenic bacteria and their near neighbors may help to understand the genetic or ecological bases which led to their pathogenic behavior. The family comprises zoonotic pathogenic species belonging to the genus as well as the environmental genus for which some species are considered as opportunistic pathogens. Here, we used a phylogenomic approach including a set of 145 genomes representative of the family diversity and more than 40 genomes of the order to infer the taxonomic relationships between the family's species. Our results clarified some unresolved phylogenetic ambiguities, conducting to the exclusion of spp. out of the family and the positioning of all spp. as a single genomic species within the current species diversity. Additional analyses also revealed that spp. separate into two clades, one comprising mostly environmental species while the other one includes the species considered as pathogens ( spp.) or opportunistic pathogens (mainly , , and ). Finally, we show that is undergoing a beginning of genome reduction suggestive of an ongoing ecological niche specialization, and that some lineages of and may shift toward an adaption to the human host.
PubMed: 32082266
DOI: 10.3389/fmicb.2019.03083 -
BMC Cancer Nov 2021Children with acute lymphoblastic leukemia (ALL) undergoing chemotherapy experience a relatively high risk of infection. And the disturbance of gut microbiota is... (Observational Study)
Observational Study
BACKGROUND
Children with acute lymphoblastic leukemia (ALL) undergoing chemotherapy experience a relatively high risk of infection. And the disturbance of gut microbiota is generally believed to impair intestinal barrier function and may induce bacterial infections and inflammation. The study aimed to investigate the alterations in the gut microbiota and assess its relationship with chemotherapy-induced pneumonia in pediatric ALL patients.
METHODS
We conducted a case-control study with 14 cases affected by pneumonia and 44 unaffected subjects and characterized the physiological parameters and gut microbiota by microarray-based technique.
RESULTS
There were significant differences in α- and β-diversity in the affected group compared with the control group. At species level, the LEfSe analysis revealed that Enterococcus malodoratus, Ochrobactrum anthropi and Actinomyces cardiffensis were significantly abundant in the affected subjects. A receiver operating characteristic (ROC) curve yielded the area under the curve (AUC) of 0.773 for classification between the two groups. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in the bacterial secretion system were more enriched in the affected group than in the control group.
CONCLUSIONS
Gut microbiota alteration was associated with chemotherapy-induced pneumonia in pediatric ALL patients, which provided a new perspective on the personalized clinical care of pediatric ALL.
Topics: Adolescent; Antineoplastic Agents; Case-Control Studies; Child; Dysbiosis; Feces; Female; Gastrointestinal Microbiome; Humans; Induction Chemotherapy; Male; Pneumonia; Precursor Cell Lymphoblastic Leukemia-Lymphoma
PubMed: 34749705
DOI: 10.1186/s12885-021-08917-y -
3 Biotech Feb 2020The aim of the study was to examine the influence of single and consortia treatments of drought tolerant rhizobacteria producing ACC deaminase together with additional...
The aim of the study was to examine the influence of single and consortia treatments of drought tolerant rhizobacteria producing ACC deaminase together with additional plant growth promoting (PGP) characteristics on finger millet growth, antioxidant and nutrient concentration under water-stressed and irrigated (no stress) conditions. These rhizobacteria belong to the sp. spp. spp. and sp. The single inoculant of RAA3 () and a consortium inoculant of four bacteria, i.e., DPC9 (), DPB13 (), DPB15 () and DPB16 (), significantly boosted the overall growth parameters and nutrient concentrations in leaves of finger millet. Moreover, elevated levels of the reactive oxygen species scavenging enzymes-superoxide dismutase (17.3%, 11.6%), guaiacol peroxidase (38.7%, 22.2%), catalase (33.7%, 21.3%) and ascorbate peroxidase (18.2%, 10.0%); cellular osmolytes-proline (41.5%, 25.0%), phenol (44.5%, 37.5%); higher leaf chlorophyll (64.4%, 30.8%) and a reduced level of hydrogen peroxide (50.7%, 59.5%) and malondialdehyde (48.4%,72.5%) were noted, respectively, after single inoculation of RAA3 and a consortium treatment by strains DPC9 + DPB13 + DPB15 + DPB16, in contrast with non-treated plants mainly under water-stressed conditions. This finding clearly illustrates that PGPB that express ACC deaminase along with additional PGP traits could be an efficient approach for improving plant health in environments, where agricultural practices are reliant on rain for water.
PubMed: 32030334
DOI: 10.1007/s13205-019-2046-4 -
Current Microbiology Apr 2021Termites are a large and important group of insects in terrestrial ecosystems that decompose lignocelluloses. Among these, Microcerotermes diversus Silvestri...
Termites are a large and important group of insects in terrestrial ecosystems that decompose lignocelluloses. Among these, Microcerotermes diversus Silvestri (Termitidae) is a destructive invasive pest in many tropical and subtropical regions. In the present study, M. diversus specimens were collected from traps in Ahvaz, Bandar Abbas, Kish, and Khark Islands. Sample suspensions were prepared in 5-ml DHO and cultured on nutrient agar (NA) medium. All 47 representative bacterial isolates were evaluated for cellulolytic activity by growing them on cellulose Congo-red agar medium. Based on some key phenotypic characteristics, the isolates were tentatively identified at the genus level. These were confirmed by 16S rRNA analysis using a universal primer pair (P1/P6). Sequence alignments revealed that most of the isolates are novel species so far found in the termite guts. Results showed that some of the isolates are common for all surveyed areas. However, there were significant differences in their numbers and degree of cellulolytic activity. The species reported here for the first time for termites of Iran are Bacillus wiedmanii, B. paramycoides, Elizabethkingia anophelis, Lysinibacillus pakestanensis, Pseudomonas hibiscicola, Actinetobacter pitti, A. venetianus, and Ochrobactrum anthropi.
Topics: Animals; Bacteria; Ecosystem; Flavobacteriaceae; Iran; Isoptera; RNA, Ribosomal, 16S; Stenotrophomonas
PubMed: 33638669
DOI: 10.1007/s00284-021-02369-0 -
Two Case Reports of Ochrobactrum anthropi Bacteremia in a Tertiary Care Hospital in Northeast India.Cureus Apr 2024is a non-fermenting, Gram-negative bacillus and an emerging opportunistic pathogen. We have isolated this organism from the blood cultures of two patients, a...
is a non-fermenting, Gram-negative bacillus and an emerging opportunistic pathogen. We have isolated this organism from the blood cultures of two patients, a 53-year-old immunocompetent male presenting with an episode of mild fever post craniotomy and an 85-year-old male with chronic obstructive pulmonary disease (COPD) and urinary retention on an indwelling catheter. The organism was identified using VITEK 2 (bioMérieux, France). Both the isolates were resistant to most of the β-lactams, including cephalosporins, and sensitive to quinolones, aminoglycosides, and carbapenems.
PubMed: 38803726
DOI: 10.7759/cureus.59123 -
Development and evaluation of a triplex droplet digital PCR method for differentiation of , and BCG.Frontiers in Microbiology 2024Tuberculosis, caused by complex (MTBC), remains a global health concern in both human and animals. However, the absence of rapid, accurate, and highly sensitive...
INTRODUCTION
Tuberculosis, caused by complex (MTBC), remains a global health concern in both human and animals. However, the absence of rapid, accurate, and highly sensitive detection methods to differentiate the major pathogens of MTBC, including , , and BCG, poses a potential challenge.
METHODS
In this study, we have established a triplex droplet digital polymerase chain reaction (ddPCR) method employing three types of probe fluorophores, with targets (targeting CFP-10-ESAT-6 gene of RD1 and Rv0222 genes of RD4), (targeting CFP-10-ESATs-6 gene of RD1), and BCG (targeting Rv3871 and Rv3879c genes of ΔRD1), respectively.
RESULTS
Based on optimization of annealing temperature, sensitivity and repeatability, this method demonstrates a lower limit of detection (LOD) as 3.08 copies/reaction for , 4.47 copies/reaction for and 3.59 copies/reaction for BCG, without cross-reaction to , , , , , , , , and , and showed repeatability with coefficients of variation (CV) lower than 10%. The method exhibits strong milk sample tolerance, the LOD of detecting in spike milk was 5 × 10 CFU/mL, which sensitivity is ten times higher than the triplex qPCR. 60 clinical DNA samples, including 20 milk, 20 tissue and 20 swab samples, were kept in China Animal Health and Epidemiology Center were tested by the triplex ddPCR and triplex qPCR. The triplex ddPCR presented a higher sensitivity (11.67%, 7/60) than that of the triplex qPCR method (8.33%, 5/60). The positive rates of , , and BCG were 1.67, 10, and 0% by triplex ddPCR, and 1.67, 6.67, and 0% by triplex qPCR, with coincidence rates of 100, 96.7, and 100%, respectively.
DISCUSSION
Our data demonstrate that the established triplex ddPCR method is a sensitive, specific and rapid method for differentiation and identification of , , and BCG.
PubMed: 38946908
DOI: 10.3389/fmicb.2024.1397792 -
Environmental Science and Pollution... Aug 2020The aim of the present study was to investigate biosurfactant production ability of five different polyaromatic hydrocarbon (PAH)-metabolizing bacteria, such as...
The aim of the present study was to investigate biosurfactant production ability of five different polyaromatic hydrocarbon (PAH)-metabolizing bacteria, such as Ochrobactrum anthropi IITR07, Pseudomonas mendocina IITR46, Microbacterium esteraromaticum IITR47, Pseudomonas aeruginosa IITR48, and Stenotrophomonas maltophilia IITR87. These bacteria showed biosurfactant production using 2% glucose as rich substrate; strain IITR47 yielded the highest with 906 and 534 mg/L biosurfactant in the presence of naphthalene and crude oil as the unique carbon sources. P. aeruginosa IITR48 showed the least surface tension at 29 N/m and the highest emulsification index at 63%. The biosurfactants produced were identified as glycolipid and rhamnolipid based on Fourier transform infrared spectroscopy analysis. In particular, the biosurfactant produced by bacteria S. maltophilia IITR87 efficiently emulsified mustard oil with an E24 value of 56%. It was observed that, all five biosurfactants from these degrader strains removed 2.4-, 1.7-, 0.9-, 3.8-, and 8.3-fold, respectively, crude oil from contaminated cotton cloth. Rhamnolipid derived from IITR87 was most efficient, exhibiting highest desorption of crude oil. These biosurfactants exhibited good stability without significantly losing its emulsification ability under extreme conditions, thus can be employed for bioremediation of PAHs from diverse contaminated ecosystem. Graphical Abstract.
Topics: Actinobacteria; Bacteria; Biodegradation, Environmental; Ecosystem; Microbacterium; Petroleum; Sewage; Surface-Active Agents
PubMed: 31190304
DOI: 10.1007/s11356-019-05591-3 -
Environmental Science and Pollution... Sep 2023Hydrocarbonoclastic bacterial strains were isolated from rhizosphere of plants growing in crude oil-contaminated sites of Assam, India. These bacteria showed plant...
Impacts of rhizoremediation and biostimulation on soil microbial community, for enhanced degradation of petroleum hydrocarbons in crude oil-contaminated agricultural soils.
Hydrocarbonoclastic bacterial strains were isolated from rhizosphere of plants growing in crude oil-contaminated sites of Assam, India. These bacteria showed plant growth-promoting attributes, even when exposed to crude oil. Two independent pot trials were conducted to test the rhizodegradation ability of the bacterial consortium in combination of plants Azadirchta indica or Delonix regia in crude oil-contaminated soil. Field experiments were conducted at two crude oil-contaminated agricultural field at Assam (India), where plants (A. indica or D. regia) were grown with the selected bacterial consortium consisting of five hydrocarbonoclastic bacterial isolates (Gordonia amicalis BB-DAC, Pseudomonas aeruginosa BB-BE3, P. citronellolis BB-NA1, Rhodococcus ruber BB-VND, and Ochrobactrum anthropi BB-NM2), and NPK was added to the soil for biostimulation. The bacterial consortium-NPK biostimulation led to change in rhizosphere microbiome with enhanced degradation of petroleum hydrocarbons (PHs) in soils contaminated with crude oil. After 120 days of planting A. indica + consortium + NPK treatment, degradation of PHs was found to be up to 67%, which was 55% with D. regia with the same treatment. Significant changes in the activities of plant and soil enzymes were also noted. The shift is bacterial community was also apparent as with A. indica, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria increased by 35.35%, 26.59%, and 20.98%, respectively. In the case of D. regia, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria were increased by 39.28%, 35.79%, and 9.60%, respectively. The predicted gene functions shifted in favor of the breakdown of xenobiotic compounds. This study suggests that a combination of plant-bacterial consortium and NPK biostimulation could be a productive approach to bioengineering the rhizosphere microbiome for the purpose of commercial bioremediation of crude oil-contaminated sites, which is a major environmental issue faced globally.
Topics: Soil; Soil Pollutants; Petroleum; Hydrocarbons; Microbiota; Biodegradation, Environmental; Bacteria; Soil Microbiology
PubMed: 37535290
DOI: 10.1007/s11356-023-29033-3 -
Letters in Applied Microbiology Dec 2020The present study was planned to detect the genes encoding carbapenemases, ESBLs and class 1 integron-integrase among bacteria obtained from retail goat meat. Fermenting...
The present study was planned to detect the genes encoding carbapenemases, ESBLs and class 1 integron-integrase among bacteria obtained from retail goat meat. Fermenting and non-fermenting bacterial isolates (n = 57), recovered from 61 goat meat samples, were identified by 16S rRNA gene sequencing. Antimicrobial susceptibility of isolates was tested by the broth dilution method using ceftazidime, cefotaxime, meropenem and imipenem. Plasmids were isolated and tested for their physical characters. Plasmids were subjected to screening of carbapenemase, ESBL and intI1 gene. Conjugation assay was performed using bla -positive isolates as the donor, and Escherichia coli HB101 as the recipient. Isolates showed the high rates of resistance to ceftazidime (77·2%), cefotaxime (70·2%), meropenem (22·8%) and imipenem (17·5%). They showed variability in number and size (~1 to >20 kb) of plasmids. Among all, 1, 4, 13 and 31 isolates showed the bla , bla , bla and bla genes, respectively. The bla gene was observed in one E. coli isolate. The bla gene was detected in Stenotrophomonas maltophilia (n = 2), Acinetobacter baumannii (n = 1) and Ochrobactrum anthropi (n = 1) isolates. These isolates co-harboured the bla and bla genes. The intI1 gene was detected in 22 (38·6%) isolates, and 16 of these isolates showed the carbapenemase and/or ESBL genes. The conjugative movement of bla gene could not be proved after three repetitive mating experiments. The presence of genes encoding carbapenemases and ESBLs in bacteria from goat meat poses public health risks.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Escherichia coli; Escherichia coli Infections; Escherichia coli Proteins; Food Contamination; Goats; Humans; Integrases; Integrons; Meat; Microbial Sensitivity Tests; Plasmids; beta-Lactamases
PubMed: 32767781
DOI: 10.1111/lam.13368 -
Acta Biochimica Et Biophysica Sinica Aug 2021Vibrio natriegens is known to be the fastest-growing free-living bacterium with the potential to be a novel protein expression system other than Escherichia coli. Seven...
Vibrio natriegens is known to be the fastest-growing free-living bacterium with the potential to be a novel protein expression system other than Escherichia coli. Seven sampled genes of interest (GOIs) encoding biocatalyst enzymes, including Ochrobactrum anthropi-derived ω-transaminase (OATA), were strongly expressed in E. coli but weakly in V. natriegens using the pET expression system. In this study, we fused the C-terminal of OATA with green fluorescent protein (GFP) and obtained V. natriegens mutants that could increase both protein yield and enzyme activity of OATA as well as the other three GOIs by ultraviolet mutagenesis, fluorescence-activated cell sorting (FACS), and OATA colorimetric assay. Furthermore, next-generation sequencing and strain reconstruction revealed that the Y457 variants in the conserved site of endogenous RNA polymerase (RNAP) β' subunit rpoC are responsible for the increase in recombinant protein yield. We speculated that the mutation of rpoC Y457 may reprogram V. natriegens's innate gene transcription, thereby increasing the copy number of pET plasmids and soluble protein yield of certain GOIs. The increase in GOI expression may partly be attributed to the increase in copy number. In conclusion, GOI-GFP fusion combined with FACS is a powerful tool of forward genetics that can be used to obtain a superior expression chassis. If more high-expression-related targets are found for more GOIs, it would make the construction of next-generation protein expression chassis more time-saving.
Topics: Biotechnology; DNA-Directed RNA Polymerases; Flow Cytometry; Green Fluorescent Proteins; High-Throughput Nucleotide Sequencing; High-Throughput Screening Assays; Molecular Biology; Mutagenesis; Ochrobactrum anthropi; Plasmids; Recombinant Proteins; Transaminases; Vibrio
PubMed: 34169308
DOI: 10.1093/abbs/gmab089