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Current Microbiology Jul 2024Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter... (Review)
Review
Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.
Topics: Soil Microbiology; Proteomics; Metagenomics; Bacteria; Microbiota; Fungi; Soil; Computational Biology
PubMed: 38955825
DOI: 10.1007/s00284-024-03781-y -
Zhonghua Er Ke Za Zhi = Chinese Journal... Jul 2024To summarize the clinical manifestations, diagnosis, treatment and prognosis of acute flaccid myelitis (AFM) in children. Clinical characteristics of 4 AFM cases from...
To summarize the clinical manifestations, diagnosis, treatment and prognosis of acute flaccid myelitis (AFM) in children. Clinical characteristics of 4 AFM cases from Department of Neurology, Children's Hospital Affiliated to Capital Institute of Pediatrics, from September 2018 to November 2022, were analyzed retrospectively. The age of 4 children with AFM was 7 years, 4 years and 3 months, 7 years and 1 month, 6 years and 5 months, respectively. There were 2 boys and 2 girls. Prodromal infection status showed 3 children of respiratory tract infection and 1 child of digestive tract infection. The main manifestation was asymmetrical limb weakness after infection, and the affected limb range was from monoplegia to quadriplegia. Cranial nerve injury was involved in 1 child, no encephalopathy. Magnetic resonance imaging in the spinal cord of all 4 children showed long T1 and T2 signals, mainly involving gray matter. Cerebrospinal fluid cell-protein separation was observed in 2 children. Pathogen detected in 1 child pharyngeal swab was enterovirus D68. Antibody IgM to adenovirus was positive in the blood of 1 child. Antibody IgG against Echo and Coxsackie B virus were positive in the blood of another child. After glucocorticoid, human immunoglobulin or simple symptomatic treatment and at the same time under later rehabilitation training, muscle strength recovered to different degrees, but there were disabilities left in 3 children. AFM should be considered in children with acute and asymmetrical flaccid paralysis accompanied by abnormal magnetic resonance imaging signal in the central region of spinal cord, especially post-infection. The effective treatment is limited and the prognosis is poor.
Topics: Humans; Myelitis; Male; Female; Child; Child, Preschool; Retrospective Studies; Magnetic Resonance Imaging; Central Nervous System Viral Diseases; Neuromuscular Diseases; Enterovirus D, Human; Prognosis; Spinal Cord; Enterovirus Infections; Quadriplegia; Respiratory Tract Infections
PubMed: 38955687
DOI: 10.3760/cma.j.cn112140-20240320-00191 -
Biochemical Genetics Jul 2024Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5...
Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5 mitogenomes of Chromodorididae (Chromodoris lochi, Chromodoris colemani, Chromodoris elisabethina, Chromodoris annae and Hypselodoris whitei) were systemically investigated. The lengths of the mitogenomes sequences were 14248 bp, 14257 bp, 14252 bp, 14254 bp and 14856 bp, respectively. Most protein-coding genes (PCGs) were initiated with the common ATG codon and terminated with the TAA and TAG. We calculated Ka/Ks values for all 13 PCGs of Chromodorididae species, all ratios were less than 1, indicating selection by purification. Phylogenetic relationships were constructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all complete genomes of 50 species, primarily from the family Chromodorididae (Doridina) and 2 outgroups. This phylogenetic tree provided further additional references for the classification of the suborder Doridina. Gene rearrangement suggested a more conserved pattern of gene sequences in the superfamily Chromodoridoidea. These results and newly sequenced will contribute to a better understanding of Chromodorididae and provide reference for further phylogenetic studies.
PubMed: 38954214
DOI: 10.1007/s10528-024-10878-3 -
Current Microbiology Jul 2024Two Gram-stain-negative, facultative anaerobic, rod-shaped, motile bacterial strains, designated F26243 and F60267 were isolated from coastal sediment in Weihai, China....
Two Gram-stain-negative, facultative anaerobic, rod-shaped, motile bacterial strains, designated F26243 and F60267 were isolated from coastal sediment in Weihai, China. Strains F26243 and F60267 were grown at 4-40 °C (optimum 33 °C), pH 7.0-9.5 and pH 6.5-9.5 (optimum at pH 7.0), in the presence of 1.0-7.0% (w/v) NaCl (optimum 2.5%) and 1.0-12.0% (w/v) NaCl (optimum 2.0%), respectively. The 16S rRNA gene sequences phylogenetic analysis showed that strains F26243 and F60267 are closely related to the genus Marinobacter and exhibited the highest sequence similarities to Marinobacter salexigens HJR7 (97.7% and 98.0%, respectively), the similarity between two isolates was 96.7%. Strains F26243 and F60267 displayed genomic DNA G + C content of 53.6% and 53.8%, respectively. When compared to the M. salexigens HJR7, the average nucleotide identity (ANI) values were 83.7% and 84.1%, and the percentage of conserved proteins (POCP) values were 79.9% and 84.6%, respectively. Ubiquinone 9 (Q-9) was the only respiratory quinone detected in both isolates. The major cellular fatty acids (> 10.0%) were summed feature 3 (comprising Cω7c and/or Cω6c), C and Cω9c. The polar lipid profiles of strains F26243 and F60267 contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, aminophospholipid and one unidentified phospholipid. Based on genomic characteristics, phenotypic and chemotaxonomic, strains F26243 and F60267 represent two novel species of the genus Marinobacter, for which the names Marinobacter sediminicola sp. nov. and Marinobacter xiaoshiensis sp. nov. are proposed, the type strains are F26243 (= KCTC 92640 = MCCC 1H01345) and F60267 (= KCTC 92638 = MCCC 1H01346).
Topics: Marinobacter; Geologic Sediments; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; DNA, Bacterial; China; Bacterial Typing Techniques; Phospholipids; Sequence Analysis, DNA; Seawater
PubMed: 38954028
DOI: 10.1007/s00284-024-03782-x -
Archives of Microbiology Jul 2024Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food...
Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food substrates has become an emerging strategy. Bacteriophages have the potential to control Salmonella contamination.We have isolated and characterized a broad-spectrum Salmonella phage, SP154, which can lyse 9 serotypes, including S. Enteritidis, S. Typhimurium, S. Pullorum, S. Arizonae, S. Dublin, S. Cholerasuis, S. Chester, S. 1, 4, [5], 12: i: -, and S. Derby, accounting for 81.9% of 144 isolates. SP154 showed a short latent period (40 min) and a high burst size (with the first rapid burst size at 107 PFUs/cell and the second rapid burst size at approximately 40 PFUs/cell). Furthermore, SP154 activity has higher survival rates across various environmental conditions, including pH 4.0-12.0 and temperatures ranging from 4 to 50 °C for 60 min, making it suitable for diverse food processing and storage applications. Significant reductions in live Salmonella were observed in different foods matrices such as milk and chicken meat, with a decrease of up to 1.9 log CFU/mL in milk contamination and a 1 log CFU/mL reduction in chicken meat. Whole genome sequencing analysis revealed that SP154 belongs to the genus Ithacavirus, subfamily Humphriesvirinae, within the family Schitoviridae. Phylogenetic analysis based on the terminase large subunit supported this classification, although an alternate tree using the tail spike protein gene suggested affiliation with the genus Kuttervirus, underscoring the limitations of relying on a single gene for phylogenetic inference. Importantly, no virulence or antibiotic resistance genes were detected in SP154. Our research highlights the potential of using SP154 for biocontrol of Salmonella in the food industry.
Topics: Salmonella Phages; Whole Genome Sequencing; Animals; Salmonella; Genome, Viral; Food Microbiology; Chickens; Milk; Meat; Phylogeny
PubMed: 38953983
DOI: 10.1007/s00203-024-04061-w -
International Journal of Systematic and... Jul 2024Two novel strain pairs (HM61/HM23 and S-34/S-58) were isolated from soil and the faeces of Tibetan antelope () collected at the Qinghai-Tibet Plateau of PR China. All...
Two novel strain pairs (HM61/HM23 and S-34/S-58) were isolated from soil and the faeces of Tibetan antelope () collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus . Strains HM61 and HM23 were most closely related to THG T63 (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34 and S-58 were most closely related to MMS20-HV4-12 (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61 and S-34 were 70.6 and 72.5 mol%, respectively. Strains HM61, S-34 and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5 % as well as digital DNA-DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus . The chemotaxonomic characteristics of strains HM61 and S-34 were consistent with the genus . The major fatty acids of all four strains were -C, C 8 or C 9. For strains HM61 and S-34, MK-8(H) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61 and S-34 represent two novel species of the genus , respectively, with the names sp. nov. and sp. nov. The type strains are HM61 (=GDMCC 4.343=JCM 36399) and S-34 (=CGMCC 4.7664=JCM 33792).
Topics: Phylogeny; RNA, Ribosomal, 16S; Soil Microbiology; Base Composition; Tibet; Fatty Acids; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Feces; Antelopes; Animals; Nucleic Acid Hybridization; China; Actinomycetales; Peptidoglycan; Phospholipids
PubMed: 38953888
DOI: 10.1099/ijsem.0.006437 -
Indian Journal of Public Health Apr 2024Several sporadic cases and outbreaks of Zika virus disease have been reported from different states of India.
BACKGROUND
Several sporadic cases and outbreaks of Zika virus disease have been reported from different states of India.
OBJECTIVES
This paper explored the possibility of any ongoing transmission of Zika virus (ZIKV) in the Bhopal region of Central India, where the last outbreak of this disease was reported in 2018.
MATERIALS AND METHODS
We screened a group of 75 febrile patients who had already tested negative for the locally endemic causes of fever like dengue, chikungunya, enteric fever, malaria, and scrub typhus and two groups of asymptomatic healthy individuals represented by blood donors (n = 75) and antenatal mothers (n = 75). We tested blood samples of febrile patients for ZIKV RNA using real-time polymerase chain reaction (PCR), and for the healthy individuals, we determined anti-zika immunoglobulin G (IgG) antibodies using enzyme-linked immunosorbent assay.
RESULTS
ZIKV RNA was not detected in any of the 75 samples tested by real-time PCR assay. Among the voluntary blood donors and antenatal mothers, a total of 10 (15.38%) and 5 (6.66%) individuals were found to be seropositive for anti-ZIKV IgG antibodies, respectively. The seropositive group was found to have higher age 33.06 (±10.83) years as compared to seronegative individuals 26.60 (±5.12) years (P = 0.037).
CONCLUSION
This study, which is the first survey of seroprevalence of anti-Zika antibodies from India, reports an overall seropositivity rate of 10% for anti-Zika antibodies among the healthy population, suggesting an ongoing, low level, silent transmission of ZIKV in the local community.
Topics: Humans; India; Zika Virus Infection; Seroepidemiologic Studies; Adult; Female; Pilot Projects; Male; Zika Virus; Immunoglobulin G; Young Adult; Antibodies, Viral; Middle Aged; RNA, Viral; Adolescent; Enzyme-Linked Immunosorbent Assay; Real-Time Polymerase Chain Reaction
PubMed: 38953800
DOI: 10.4103/ijph.ijph_1098_23 -
Journal of Medical Virology Jul 2024Factor VIII and IX clotting factor concentrates manufactured from pooled plasma have been identified as potent sources of virus infection in persons with hemophilia...
Factor VIII and IX clotting factor concentrates manufactured from pooled plasma have been identified as potent sources of virus infection in persons with hemophilia (PWHs) in the 1970s and 1980s. To investigate the range and diversity of viruses over this period, we analysed 24 clotting factor concentrates for several blood-borne viruses. Nucleic acid was extracted from 14 commercially produced clotting factors and 10 from nonremunerated donors, preserved in lyophilized form (expiry dates: 1974-1992). Clotting factors were tested by commercial and in-house quantitative PCRs for blood-borne viruses hepatitis A, B, C and E viruses (HAV, HBV, HCV, HEV), HIV- types 1/2, parvoviruses B19V and PARV4, and human pegiviruses types 1 and 2 (HPgV-1,-2). HCV and HPgV-1 were the most frequently detected viruses (both 14/24 tested) primarily in commercial clotting factors, with frequently extremely high viral loads in the late 1970s-1985 and a diverse range of HCV genotypes. Detection frequencies sharply declined following introduction of virus inactivation. HIV-1, HBV, and HAV were less frequently detected (3/24, 1/24, and 1/24 respectively); none were positive for HEV. Contrastingly, B19V and PARV4 were detected throughout the study period, even after introduction of dry heat treatment, consistent with ongoing documented transmission to PWHs into the early 1990s. While hemophilia treatment is now largely based on recombinant factor VIII/IX in the UK and elsewhere, the comprehensive screen of historical plasma-derived clotting factors reveals extensive exposure of PWHs to blood-borne viruses throughout 1970s-early 1990s, and the epidemiological and manufacturing parameters that influenced clotting factor contamination.
Topics: Humans; Blood Coagulation Factors; Blood-Borne Pathogens; Blood-Borne Infections; Drug Contamination; History, 20th Century; Hemophilia A; Viruses; Polymerase Chain Reaction; Factor VIII; Time Factors
PubMed: 38953434
DOI: 10.1002/jmv.29774 -
Journal of Korean Medical Science Jul 2024A 30-year-old Korean man with myelodysplastic syndrome admitted hospital due to undifferentiated fever and recurrent skin lesions. He received combination therapy with...
A 30-year-old Korean man with myelodysplastic syndrome admitted hospital due to undifferentiated fever and recurrent skin lesions. He received combination therapy with high doses of meropenem, tigecycline and amikacin, yielding carbapenem resistant (CRKP) harboring carbapenemase (KPC)-2 from blood cultures on hospital day (HD) 23. Ceftazidime/avibactam was started at HD 37 and CRKP was eradicated from blood cultures after 5 days. However, ceftazidime/avibactam-resistant CRKP carrying KPC-44 emerged after 26 days of ceftazidime/avibactam treatment and then ceftazidime/avibactam-resistant, carbapenem-susceptible carrying KPC-135 was isolated on HD 65. The 3-D homology of KPC protein showed that hot spot changes in the omega loop could be attributed to ceftazidime/avibactam resistance and loss of carbapenem resistance. Whole genome sequencing of serial isolates supported that phenotypic variation was due to clonal evolution than clonal replacement. The treatment regimen was changed from CAZ/AVI to meropenem-based therapy (meropenem 1 g iv q 8 hours and amikacin 600 mg iv per day) starting with HD 72. CAZ/AVI-susceptible CRKP was presented again from blood cultures on HD 84, and the patient expired on HD 85. This is the first Korean report on the acquisition of ceftazidime/avibactam resistance through the emergence of variants.
Topics: Humans; Ceftazidime; Klebsiella pneumoniae; Male; Azabicyclo Compounds; Drug Combinations; Adult; Anti-Bacterial Agents; beta-Lactamases; Klebsiella Infections; Bacteremia; Microbial Sensitivity Tests; Carbapenems; Whole Genome Sequencing; Bacterial Proteins; Meropenem; Drug Resistance, Multiple, Bacterial
PubMed: 38952349
DOI: 10.3346/jkms.2024.39.e208 -
Acta Biochimica Et Biophysica Sinica Jul 2024Immune checkpoint inhibitors (ICIs) targeting programmed cell death 1/programmed cell death ligand-1 (PD-1/PD-L1) have significantly prolonged the survival of...
Immune checkpoint inhibitors (ICIs) targeting programmed cell death 1/programmed cell death ligand-1 (PD-1/PD-L1) have significantly prolonged the survival of advanced/metastatic patients with lung cancer. However, only a small proportion of patients can benefit from ICIs, and clinical management of the treatment process remains challenging. Glycosylation has added a new dimension to advance our understanding of tumor immunity and immunotherapy. To systematically characterize anti-PD-1/PD-L1 immunotherapy-related changes in serum glycoproteins, a series of serum samples from 12 patients with metastatic lung squamous cell carcinoma (SCC) and lung adenocarcinoma (ADC), collected before and during ICIs treatment, are firstly analyzed with mass-spectrometry-based label-free quantification method. Second, a stratification analysis is performed among anti-PD-1/PD-L1 responders and non-responders, with serum levels of glycopeptides correlated with treatment response. In addition, in an independent validation cohort, a large-scale site-specific profiling strategy based on chemical labeling is employed to confirm the unusual characteristics of IgG N-glycosylation associated with anti-PD-1/PD-L1 treatment. Unbiased label-free quantitative glycoproteomics reveals serum levels' alterations related to anti-PD-1/PD-L1 treatment in 27 out of 337 quantified glycopeptides. The intact glycopeptide EEQFN STYR (H3N4) corresponding to IgG4 is significantly increased during anti-PD-1/PD-L1 treatment (FC=2.65, =0.0083) and has the highest increase in anti-PD-1/PD-L1 responders (FC=5.84, =0.0190). Quantitative glycoproteomics based on protein purification and chemical labeling confirms this observation. Furthermore, obvious associations between the two intact glycopeptides (EEQFN STYR (H3N4) of IgG4, EEQYN STFR (H3N4F1) of IgG3) and response to treatment are observed, which may play a guiding role in cancer immunotherapy. Our findings could benefit future clinical disease management.
PubMed: 38952341
DOI: 10.3724/abbs.2024110