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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 -
, 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 -
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 -
Revista Argentina de Microbiologia 2022Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of...
Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of infections by this microorganism are scarce, it has been associated with a wide spectrum of infectious diseases. The case of an elderly man with a lower corneal abscess, in which Dolosigranulum pigrum was isolated, is described. The microorganism was identified by mass spectrometry (MALDI-TOF MS) and by the sequencing of the 16S rRNA gene. Furthermore, the presumptive identification of the causative agent was achieved by using key phenotypic tests such as the cluster arrangement in Gram stain, the negative catalase test, the production of pyrrolidonyl arylamidase and leucine aminopeptidase activity, the growth in 6.5% NaCl and esculin hydrolysis. The data from the literature (and the present case) support the association of the microorganism with ocular infections, which often take a destructive course, mainly in elderly patients.
Topics: Abscess; Aged; Carnobacteriaceae; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Male; RNA, Ribosomal, 16S
PubMed: 34895780
DOI: 10.1016/j.ram.2021.10.002 -
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 -
Veterinary Sciences Nov 2022is a facultative anaerobic Gram-positive coccus belonging to the Rothia genus of the family. While is considered an opportunistic pathogen, to date few studies have...
is a facultative anaerobic Gram-positive coccus belonging to the Rothia genus of the family. While is considered an opportunistic pathogen, to date few studies have investigated its pathogenicity and drug resistance. In January 2022, chickens at a poultry farm in China's Xinjiang Uygur Autonomous Region became ill and died. Treatment with commonly used Chinese medicines and antibiotics was ineffective, causing economic losses to the poultry farm. In order to determine the cause of the disease in these poultry farm chickens, the isolation and identification of the pathogens in the livers and other internal organs of the sick and dead chickens were performed. Further, animal pathogenicity tests, antibiotic susceptibility tests, and the detection of antibiotic resistance genes were carried out to analyze the pathogenicity and drug resistance of the identified pathogens. A Gram-positive coccus was isolated from the livers of the diseased chickens. The isolate was resistant to 17 antibiotics, including ciprofloxacin, chloramphenicol, and florfenicol, and was only sensitive to penicillin, amikacin, and tigecycline, to varying degrees. The results of the drug resistance gene testing indicated that the isolated bacterium carried 13 kinds of resistance genes. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, morphological observations, biochemical tests, and 16S rRNA gene sequence analysis were performed on the isolated bacterium, and it was determined that the isolated bacterial strain was . The animal pathogenicity tests showed that the isolate caused feather loss and death in chicks; the clinical symptoms and necropsy lesions of the test chicks were consistent with those observed in the farmed chickens. A review of the literature revealed that, to date, there are no reports of infection with in chickens. Thus, in this study, was isolated from chickens for the first time and an investigation of the biological characteristics of the bacterium was carried out in order to provide a reference for the clinical treatment, prevention, and control of infection.
PubMed: 36548814
DOI: 10.3390/vetsci9120653 -
The Journal of Veterinary Medical... Sep 2023Melissococcus plutonius is a Gram-positive lanceolate coccus that is the causative agent of European foulbrood, an important bacterial disease of honey bee brood.... (Review)
Review
Melissococcus plutonius is a Gram-positive lanceolate coccus that is the causative agent of European foulbrood, an important bacterial disease of honey bee brood. Although this bacterium was originally described in the early 20th century, a culture method for this bacterium was not established until more than 40 years after its discovery due to its fastidious characteristics, including the requirement for high potassium and anaerobic/microaerophilic conditions. These characteristics were considered to be common to the majority of M. plutonius strains isolated worldwide, and M. plutonius was also thought to be genetically homologous or clonal for years. However, non-fastidious variants of this species (designated as atypical M. plutonius) were very recently identified in Japan. Although the morphology of these unusual strains was similar to that of traditionally well-known M. plutonius strains, atypical strains were genetically very different from most of the M. plutonius strains previously isolated and were highly virulent to individual bee larva. These atypical variants were initially considered to be unique to Japan, but were subsequently found worldwide; however, the frequency of isolation varied from country to country. The background of the discovery of atypical M. plutonius in Japan and current knowledge on atypical strains, including their biochemical and culture characteristics, virulence, detection methods, and global distribution, are described in this review. Remaining mysteries related to atypical M. plutonius and directions for future research are also discussed.
Topics: Bees; Animals; Virulence; Larva; Enterococcaceae; Bacterial Infections
PubMed: 37460304
DOI: 10.1292/jvms.23-0180 -
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 -
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