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Systematic and Applied Microbiology Sep 2021A Gram-positive, anaerobic coccus isolated from a human surgical site infection was previously shown to belong to an unknown species of the genus Peptoniphilus initially... (Review)
Review
Peptoniphilus nemausensis sp. nov. A new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names.
A Gram-positive, anaerobic coccus isolated from a human surgical site infection was previously shown to belong to an unknown species of the genus Peptoniphilus initially proposed as 'Peptoniphilus nemausus' sp. nov., based on both 16S rRNA gene sequence identity of 97.9% with the most closely related species Peptoniphilus coxii and an individualized phylogenetic branching within the genus Peptoniphilus. A polyphasic characterization of the novel species is proposed herein. Whole genome sequence analysis showed an average nucleotide identity value of 84.75% and digital DNA-DNA hybridization value of 28.9% against P. coxii type strain. The strain displayed unique features among members of the genus Peptoniphilus, as it was able to hydrolyze aesculin, and produced acetate as the major metabolic end-product without associated production of butyrate. Growth was observed under microaerophilic conditions. From all these data, the isolate is confirmed as belonging to a new Peptoniphilus species, for which the name Peptoniphilus nemausensis sp. nov. is proposed. The type strain is 1804121828 (=LMG 31466 = CECT 9935). A database survey using a highly polymorphic partial sequence of the 16S rRNA gene of P. nemausensis revealed P. nemausensis to be a particularly rare skin-associated species in humans. An emendated description of the Peptoniphilus genus is proposed based on a review of the characteristics of the 12 new species with validly published names since the genus description in 2001 and of P. nemausensis. Finally, the relationships between members of the genus Peptoniphilus were explored based on whole genome sequence analysis in order to clarify the taxonomic status of not yet validly published species showing that three pairs of species should be considered as synonyms: Peptoniphilus timonensis and 'Peptoniphilus phoceensis', Peptoniphilus lacydonensis and 'Peptoniphilus rhinitidis', Peptoniphilus tyrrelliae and Peptoniphilus senegalensis.
Topics: Anaerobiosis; Bacterial Typing Techniques; Firmicutes; Humans; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Surgical Wound Infection
PubMed: 34385044
DOI: 10.1016/j.syapm.2021.126235 -
Nature Jan 2020The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the...
The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E) model.
Topics: Amino Acids; Archaea; Eukaryotic Cells; Evolution, Molecular; Genome, Archaeal; Geologic Sediments; Lipids; Models, Biological; Phylogeny; Prokaryotic Cells; Symbiosis
PubMed: 31942073
DOI: 10.1038/s41586-019-1916-6 -
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 -
Medecine Et Maladies Infectieuses Feb 2019Veillonella parvula is an anaerobic Gram-negative coccus rarely involved in bone and joint infections.
OBJECTIVES
Veillonella parvula is an anaerobic Gram-negative coccus rarely involved in bone and joint infections.
PATIENTS AND METHOD
We report the case of a Veillonella parvula vertebral osteomyelitis (VO) in a female patient without any risk factor.
RESULTS
The 35-year-old patient was immunocompetent and presented with Veillonella parvula VO. She was admitted to hospital for inflammatory lower back pain. The discovertebral sample was positive for Veillonella parvula. Literature data on Veillonella VO is scarce. Reported cases usually occurred in immunocompromised patients. Diagnosis delay can be up to four months. Patients are usually afebrile. Outcome with antimicrobial treatment alone is favorable in half of cases. Other patients must undergo surgery.
CONCLUSIONS
Veillonella VO may occur in immunocompetent patients and have a clinical spectrum of mechanical lower back pain.
Topics: Adult; Discitis; Female; Gram-Negative Bacterial Infections; Humans; Immunocompetence; Lumbar Vertebrae; Osteomyelitis; Veillonella
PubMed: 30385069
DOI: 10.1016/j.medmal.2018.10.001 -
PloS One 2020Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and...
Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and infection is one of the most common reasons for diabetes-related hospitalizations and amputations. In this study, we examined how DFU microbiomes respond to initial sharp debridement and offloading and how the initial composition associates with 4 week healing outcomes. We employed 16S rRNA next generation sequencing to perform microbial profiling on 50 samples collected from 10 patients with vascularized neuropathic DFUs. Debrided wound samples were obtained at initial visit and after one week from two DFU locations, wound bed and wound edge. Samples of the foot skin outside of the wounds were also collected for comparison. We showed that DFU wound beds are colonized by a greater number of distinct bacterial phylotypes compared to the wound edge or skin outside the wound. However, no significant microbiome diversity changes occurred at the wound sites after one week of standard care. Finally, increased initial abundance of Gram-positive anaerobic cocci (GPAC), especially Peptoniphilus (p < 0.05; n = 5 subjects), was associated with impaired healing; thus, GPAC's abundance could be a predictor of the wound-healing outcome.
Topics: Aged; Bacteria, Anaerobic; Debridement; Diabetic Foot; Female; Foot Ulcer; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Male; Microbiota; Middle Aged; Predictive Value of Tests; Treatment Outcome; Wound Healing
PubMed: 31978071
DOI: 10.1371/journal.pone.0227006 -
Current Research in Microbial Sciences 2022() is a facultative anaerobic, coccus-shaped halophilic lactic acid-producing bacterium previously detected and cultured in various salty foods and credited for...
() is a facultative anaerobic, coccus-shaped halophilic lactic acid-producing bacterium previously detected and cultured in various salty foods and credited for beneficial effects on human health. In this study, we investigated the presence of in human samples using a polyphasic approach including scanning electron microscopy, molecular biology methods and microbial culture. This unique investigation yielded the unprecedented presence of in human feces samples, thus enriching the repertoire of halophilic microorganisms colonizing the human gastrointestinal tract with the isolation and culture of for the first time in humans. Using the E-test strips, the MIC was assessed for T. strain CSURQ6002: rifampicin (MIC at 0.002 μg/mL), benzylpenicillin (MIC at 0.094 μg/mL), amoxicillin (MIC at 0.5 μg/mL), erythromycin (MIC at 2 μg/mL), clindamycin (MIC at 4 μg/mL), and vancomycin (MIC at 8 μg/mL). However, this strain showed a MIC up to 256 μg/mL for ciprofloxacin, fosfomycin, doxycyclin, imipenem, and colistin. profiling derived from whole genome sequencing (NCBI accession number: PRJNA780809), was confirmed. This discovery suggested that was part of the human digestive microbiota and that its potential role on human health should be considered.
PubMed: 35243447
DOI: 10.1016/j.crmicr.2022.100112 -
IDCases 2022
PubMed: 35127449
DOI: 10.1016/j.idcr.2022.e01417 -
, an oral pathobiont associated with colorectal cancer, epigenetically reprograms human colonocytes.Gut Microbes Dec 2023Recently, an intestinal dysbiotic microbiota with enrichment in oral cavity bacteria has been described in colorectal cancer (CRC) patients. Here, we characterize and...
Recently, an intestinal dysbiotic microbiota with enrichment in oral cavity bacteria has been described in colorectal cancer (CRC) patients. Here, we characterize and investigate one of these oral pathobionts, the Gram-positive anaerobic coccus . We identified two phylotypes (A and B) exhibiting different phenotypes and adhesion capabilities. We observed a strong association of phylotype A with CRC, with its higher abundance in feces and in tumoral tissue compared with the normal homologous colonic mucosa, which was associated with a distinct methylation status of patients. By developing an hypoxic co-culture system of human primary colonic cells with anaerobic bacteria, we show that phylotype A alters the DNA methylation profile promoters of key tumor-suppressor genes, oncogenes, and genes involved in epithelial-mesenchymal transition. In colonic mucosa of CRC patients carrying phylotype A, we found similar DNA methylation alterations, together with significant enrichment of differentially expressed genes in pathways involved in inflammation, cell adhesion, and regulation of actin cytoskeleton, providing evidence of possible role in the carcinogenic process.
Topics: Humans; Gastrointestinal Microbiome; Firmicutes; Bacteria; Colorectal Neoplasms
PubMed: 37842920
DOI: 10.1080/19490976.2023.2265138 -
BMJ Case Reports Apr 2013Acute cholecystitis is a common inflammatory condition of the gallbladder caused most commonly by Escherichia coli, Enterococcus, and Klebsiella organisms. Streptococcus...
Acute cholecystitis is a common inflammatory condition of the gallbladder caused most commonly by Escherichia coli, Enterococcus, and Klebsiella organisms. Streptococcus bovis is a Gram-positive, catalase-negative, anaerobic coccus found as a commensal inhabitant of the digestive system in 16% of healthy people. We report a rare case of acute cholecystitis caused by S bovis and discuss its implications with regard to the two known S bovis biotypes (I & II) both of which are associated with a number of other gastrointestinal diseases.
Topics: Acute Disease; Anti-Bacterial Agents; Cholecystitis; Diagnosis, Differential; Diagnostic Imaging; Humans; Male; Middle Aged; Streptococcal Infections; Streptococcus bovis
PubMed: 23605823
DOI: 10.1136/bcr-2013-008581 -
International Journal of Systematic and... Sep 2023A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene...
A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene sequencing yielded results indicative of CBA3646 representing a member of the genus , with the species most closely related to it being DSM 20463, with a similarity of 94.79 %. DNA-DNA relatedness and average nucleotide identity values between CBA3646 and DSM 20463 were 21.4 and 67.6 %, respectively. CBA3646 has a circular chromosomal genome of 1 709 189 bp (45.5 mol% DNA G+C content), containing 1652 genes in total, 1584 predicted protein-coding genes, 3 complete rRNA loci and 47 tRNA genes. The cells were non-motile diplococci, catalase-positive and oxidase-negative. Growth of CBA3646 was observed at 20-40 °C (optimal temperature, 35 °C) and in the presence of 0-4 % (w/v) NaCl (optimum concentration, 1 %). The major fatty acids (>10 %) of CBA3646 were C, Cω9 and Cω9 dimethyl acetal, with its major polar lipids being diphosphatidylglycerol and phosphatidylglycerol. The elucidated phylogenetic, physiological, chemotaxonomic and molecular properties are indicative of strain CBA3646 representing a novel species of the genus , or which the name sp. nov. is proposed. The type strain is CBA3646 (= KACC 22890 = JCM 35845).
Topics: Horses; Animals; Coloring Agents; Anaerobiosis; Base Composition; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Gram-Positive Cocci; Feces; Clostridiales
PubMed: 37750780
DOI: 10.1099/ijsem.0.006053