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International Journal of Systematic and... Mar 2022An anaerobic bacterial strain, designated AMB_01, recovered from mesophilic propionate enrichment of a high-ammonia biogas digester, was characterised using phenotypic...
An anaerobic bacterial strain, designated AMB_01, recovered from mesophilic propionate enrichment of a high-ammonia biogas digester, was characterised using phenotypic and molecular taxonomic methods. Cells of AMB_01 are coccus-shaped and often occur arranged as diplococci or sarcina. Growth occurred at 20-45 °C, initial pH 5.5-8.5 and with up to 0.7 M NHCl, with optimum growth at 37-42 °C and pH 8.0. AMB_01 achieved high cell density and highest acetate production when grown on carbohydrates, including monomers, disaccharides and polysaccharides, such as glucose, maltose, cellobiose and starch. The strain was also able to use amino acids and some organic acids and alcoholic compounds for growth. Acetate was formed as the main product and yeast was not required for growth. The major cellular fatty acids were summed feature 4 (iso-CI and/or anteiso-CB), Cω7, C, C and summed feature 3 (Cω7 and/or iso-C 2OH). The highest 16S rRNA gene sequence similarity found was with (96.6 %), within the family , phylum Bacillota (Firmicutes). The genomic DNA G+C content was 29.0 mol%. An almost complete set of genes for the acetyl-CoA pathway was found. Genome comparisons between AMB_01 and close relatives showed highest digital DNA-DNA hybridisation to (23 %), highest average nucleotide identity with genome nucleotide and amino acid sequences to (72 and 73 %, respectively) and highest average nucleotide identity (87 %) with , indicating that AMB_01 represents a novel species. Analysis of genomic, chemotaxonomic, biochemical and physiological data confirmed that strain AMB_01 represents a novel species, for which the name sp. nov. is proposed. The type strain is AMB_01 (=DSM 110247=JCM 39107 ).
Topics: Acetates; Ammonium Compounds; Bacterial Typing Techniques; Base Composition; Biofuels; DNA, Bacterial; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35312473
DOI: 10.1099/ijsem.0.005328 -
Cureus Nov 2023() is a gram-positive anaerobic coccus endemic to the oral cavity and intestinal tract. We report a case of pyogenic spondylitis caused by and summarize the clinical...
() is a gram-positive anaerobic coccus endemic to the oral cavity and intestinal tract. We report a case of pyogenic spondylitis caused by and summarize the clinical features of previous case reports. An 81-year-old man with a history of lumbar vertebral compression fracture two years previously presented to the emergency department with low back pain. He was clinically diagnosed with pyogenic spondylitis due to difficulty in moving his body, spinal tapping pain, and signs of inflammation. He was hospitalized, and aerobic and anaerobic blood culture samples were collected, but the results were negative. Computed tomography and magnetic resonance imaging revealed inflammation in the second and third lumbar vertebrae and L2/3 and L3/4 intervertebral discs, and culture of the infected disc biopsy showed growth. After six weeks of treatment with ampicillin-sulbactam and ampicillin, the patient's symptoms improved, and he was discharged. During hospitalization, he was diagnosed with periodontitis and type 2 diabetes; his dentures were adjusted, and he was started on an oral hypoglycemic agent. Pyogenic spondylitis caused by tends to be associated with oral infections. This case illustrates the importance of appropriate detection and treatment of the source of infection to prevent recurrence.
PubMed: 38090456
DOI: 10.7759/cureus.48665 -
International Journal of Systematic and... Jan 2021Two strains of previously unknown Gram-negative cocci, T1-7 and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical...
Two strains of previously unknown Gram-negative cocci, T1-7 and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical phenotypic characteristics of members of the genus , including catalase production. Sequencing of their 16S rRNA genes confirmed that they belong to genus . Under anaerobic conditions, the two strains produced acetic acid and propionic acid as metabolic end-products in a trypticase-yeast extract-haemin medium containing 1 % (w/v) glucose, 1 % (w/v) fructose and 1 % (v/v) sodium lactate. Comparative analysis of the 16S rRNA, , and gene sequences revealed that the two strains are phylogenetically homogeneous and comprise a distinct, novel lineage within the genus . The sequences from the two strains shared the highest similarity, at 99.9, 95.8, 96.9 and 96.7 %, using the partial 16S rRNA, , and gene sequences, respectively, with the type strains of the two most closely related species, ATCC 17748 and JCM 31738. Furthermore, strain T1-7 shared the highest average nucleotide identity (ANI) value (94.06 %) with type strain of the most closely related species, . At the same time, strain T1-7 showed the highest digital DNA-DNA hybridization (dDDH) value (55.5 %) with the type strain of . The two strains reported in this study were distinguished from the previously reported species from the genus based on catalase production, partial , and sequences, average ANI and dDDH values. Based on these observations, the two strains represent a novel species, for which the name sp. nov. is proposed. The type strain is T1-7 (JCM 33966=CCUG 74597).
Topics: Bacterial Typing Techniques; Base Composition; Child; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Humans; Japan; Mouth; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Veillonella
PubMed: 33263509
DOI: 10.1099/ijsem.0.004583 -
Antibiotics (Basel, Switzerland) Oct 2023is a catalase-negative, facultative anaerobic, Gram-positive coccus that is commensal in humans but can become opportunistic and cause severe infectious diseases, such...
is a catalase-negative, facultative anaerobic, Gram-positive coccus that is commensal in humans but can become opportunistic and cause severe infectious diseases, such as infective endocarditis. Few studies have tested the antimicrobial susceptibility of . We tested its antimicrobial susceptibility to 27 drugs and defined the resistant genes using PCR in 58 strains, including 52 clinical isolates and six type strains. The type strains and clinical isolates included 22 , 18 (GH) group (genetically indistinguishable from and ), 13 , three , and two . No strain was resistant to beta-lactams and vancomycin. In total, 6/22 (27.3%) strains were erythromycin- and clindamycin-resistant -positive, whereas 4/18 (22.2%) in the GH group, 7/13 (53.8%) , and 1/3 (33.3%) of the strains were erythromycin-non-susceptible - or -positive and clindamycin-susceptible. The MIC of minocycline and the ratios of -positive strains varied across the different species-: 2 µg/mL and 27.3% (6/22); GH group: 8 µg/mL and 27.8% (5/18); : 8 µg/mL and 46.2% (6/13), respectively. Levofloxacin resistance was significantly higher in (9/13 69.2%) than in (2/22 9.1%). Levofloxacin resistance was associated with a substitution at serine 83 for leucine, phenylalanine, or tyrosine in GyrA. The mechanisms of resistance to erythromycin and clindamycin differed across species. In addition, the rate of susceptibility to levofloxacin differed across sp., and the quinolone resistance mechanism was caused by mutations in GyrA alone.
PubMed: 37887239
DOI: 10.3390/antibiotics12101538 -
Clinical Laboratory Jul 2021Staphylococcus aureus is a gram-positive coccus forming grape like clusters performing both aerobic and anaerobic respiration. Most strains of S. aureus ferment mannitol... (Review)
Review
BACKGROUND
Staphylococcus aureus is a gram-positive coccus forming grape like clusters performing both aerobic and anaerobic respiration. Most strains of S. aureus ferment mannitol and they form characteristic golden yellow colonies. They produce catalase, coagulase, and extracellular cell clumping factor. Some strains can also produce capsules. It is a major commensal bacterium and a human pathogen that causes a wide range of clinical infections including abscesses of various organs, pneumonia, osteomyelitis, endocarditis, arthritis, and sepsis. S. aureus is the key organism for food poisoning and it is the third most important cause of food borne disorders in the world.
METHODS
We reviewed all the relevant literature available on PubMed, Web of Science, and Google Scholar. We selected different scientific studies and reports published in English language which addressed prevalence, pathogenesis, burden and laboratory diagnosis methods of S. aureus to compile the current review.
RESULTS
Staphylococcus aureus has an outstanding ability to acquire resistance to most classes of antimicrobial agents. This successful and adaptable resistance has made treatment and control of staphylococcal infections increasingly difficult. Expression of virulence factors of S. aureus is controlled by bacterial cell density and many environmental factors such as pH, oxygen, and carbon dioxide. There are different mechanisms that microorganisms use to prevent attack by antimicrobial agents. These include limiting uptake of the drug, modification of the drug target, inactivation of the drug, and active efflux of the drug. Specimens collected for diagnosis of S. aureus infection depend on the type of infection. The samples for diagnosis are pus, sputum, blood, feces, vomit and the remains of suspected food, and nasal swab for the detection of carriers. Gram stain, culture, biochemical tests, serological tests and molecular techniques are the common laboratory diagnosis methods.
CONCLUSIONS AND RECOMMENDATIONS
Multidrug resistant S. aureus strains are emerging and current antibiotics are not efficacious against such strains. Both active and passive immunization strategies have thus far failed to show efficacy in humans. Therefore, infection preventive measures, and further research is required to develop vaccines and antibiotics to target this pathogen.
Topics: Anti-Bacterial Agents; Coagulase; Delivery of Health Care; Humans; Methicillin-Resistant Staphylococcus aureus; Staphylococcal Infections; Staphylococcus aureus
PubMed: 34258960
DOI: 10.7754/Clin.Lab.2020.200930 -
International Journal of Systematic and... Jun 2021An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490 was isolated from swine faeces. 16S rRNA gene sequence-based...
An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490 was isolated from swine faeces. 16S rRNA gene sequence-based phylogenetic analysis indicated that the isolate belongs to the genus and that the most closely related species is WAL 10418 (=KCTC 5947, 97.22 % 16S rRNA gene sequence similarity). Whole genome sequence analysis determined that the DNA G+C content of strain AGMB00490 was 31.2 mol% and moreover that the genome size and numbers of tRNA and rRNA genes were 2 129 517 bp, 34 and 10, respectively. Strain AGMB00490 was negative for oxidase and urease; positive for catalase, indole production, arginine arylamidase, leucine arylamidase, tyrosine arylamidase and histidine arylamidase; and weakly positive for phenylalanine arylamidase and glycine arylamidase. The major cellular fatty acids (>10 %) of the isolate were determined to be C and C ω9. Strain AGMB00490 produced acetic acid as a major end product of metabolism. Accordingly, phylogenetic, physiologic and chemotaxonomic analyses revealed that strain AGMB00490 represents a novel species for which the name sp. nov. is proposed. The type strain is AGMB00490 (=KCTC 15944=NBRC 114159).
Topics: Animals; Bacteria, Anaerobic; Bacterial Typing Techniques; Base Composition; Clostridiales; DNA, Bacterial; Fatty Acids; Feces; Gram-Positive Cocci; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Swine
PubMed: 34125664
DOI: 10.1099/ijsem.0.004836 -
International Journal of Systematic and... Oct 2020A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was...
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C 7/C 6 and C were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31 shared 96.8 % similarity with JCM 19527 and 95.9 % with EM0302. Digital DNA-DNA hybridization values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31 as a representative of a novel species in the genus , for which the name sp. nov. is proposed. The type strain is CQN31 (=KCTC 62447=MCCC 1H00309).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Lakes; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32886590
DOI: 10.1099/ijsem.0.004436 -
Granulicatella seriolae sp. nov., a Novel Facultative Anaerobe Isolated from Yellowtail Marine Fish.Current Microbiology Nov 2023A bacterial strain, designated as S8, was isolated from the gut contents of Seriola quinqueradiata from the coastal sea area of Jeju Island, South Korea. The strain is a...
A bacterial strain, designated as S8, was isolated from the gut contents of Seriola quinqueradiata from the coastal sea area of Jeju Island, South Korea. The strain is a Gram-staining positive, non-motile, non-spore-forming, facultative anaerobic coccus. Optimal growth was observed at 30 °C, pH 8.0-9.0, and 0-0.5% w/v NaCl, under anaerobic conditions. The predominant fatty acids were C ω9c, C, C, and C ω9c, while quinone was not detected. The genome was 2,224,566 bp long, with a GC content of 38.2%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain S8 had 96.2% similarity with Granulicatella adiacens ATCC 49175, its closest known species according to nomenclature. The DNA-DNA hybridization (dDDH), average nucleotide identity, and average amino acid identity values between strain S8 and G. adiacens ATCC 49175 were 25.7%, 85.5%, and 77.2%, respectively, all of which fall below the recommended threshold for species differentiation. Based on genomic, phenotypic, and phylogenetic evidence, we propose that strain S8 should be a novel species within the genus Granulicatella, for with the name Granulicatella seriolae sp. nov. is proposed. The type strain is S8 (KCTC 43438 = JCM 35604).
Topics: Animals; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Fatty Acids; Bacteria; Streptococcus; Fishes; Perciformes; Nucleic Acid Hybridization; DNA; DNA, Bacterial; Bacterial Typing Techniques
PubMed: 38001383
DOI: 10.1007/s00284-023-03523-6 -
Indian Journal of Pathology &... 2023Sarcina Ventriculi is a gram-positive anaerobic coccus rarely reported in patients with delayed gastric emptying, emphysematous gastritis, gastric ulcers, and...
Sarcina Ventriculi is a gram-positive anaerobic coccus rarely reported in patients with delayed gastric emptying, emphysematous gastritis, gastric ulcers, and perforation. So far, less than 30 cases of sarcina isolated from the stomach have been reported. Herein, we describe a case of a 66-year-old male with a history of persistent epigastric pain and regurgitation. The upper gastrointestinal (GI) endoscopy revealed gastric erythema, edema, ulceration, and food bezoar. A gastric biopsy was done to rule out lymphoma. On histopathological examination, sarcina Ventriculi was identified. This organism is likely to get underreported as it may not be that obvious on routinely stained biopsies. Given its association with life-threatening illness such as emphysematous gastritis and perforation, awareness of this organism is important. It's presence in gastric biopsies must be mentioned in the report and should prompt the clinicians to investigate further for functional causes of delayed gastric emptying and gastric outlet obstruction like occult malignancy.
Topics: Male; Humans; Aged; Sarcina; Gastroparesis; Gastritis; Endoscopy, Gastrointestinal
PubMed: 36656232
DOI: 10.4103/ijpm.ijpm_1007_21 -
Archives of Microbiology Nov 2021Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella...
Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella massiliensis Marseille-P3249, was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249 is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C (34%), C (28%), C (15%) and C (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93, its phylogenetically closest species with standing in nomenclature. Its digital DNA-DNA hybridization (dDDH) and OrthoANI values with G. bergeri of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species Gemella massilienis sp. nov., strain Marseille-P3249 (= CSUR P3249 = DSMZ 103940).
Topics: Base Composition; DNA, Bacterial; Fatty Acids; Gemella; Humans; Male; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sputum
PubMed: 34420080
DOI: 10.1007/s00203-021-02493-2