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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 -
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 -
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 -
Current Medical Research and Opinion Aug 2022belongs is a gram-positive anaerobic coccus (GPAC), which can cause bacterial vaginitis. However, only a few studies have reported severe infection of . This study...
BACKGROUND
belongs is a gram-positive anaerobic coccus (GPAC), which can cause bacterial vaginitis. However, only a few studies have reported severe infection of . This study presented the first case of severe infection of during pregnancy. It aimed to help to fill the gap in the literature, find out the factors that accelerate infection and discuss the significance of the GPAC test.
CASE PRESENTATION
A 35-year-old woman was admitted due to unbearable abdominal pain with dilation of the cervical opening at 22+ weeks of gestation. A blood test revealed electrolyte disturbance and hypoproteinemia. A day before admission, the patient developed pain in the lower abdomen accompanied by yellow-green vaginal discharge. Two hours after admission, the patient suddenly presented with hyperpyrexia and chills. Timely and adequate antibiotic and cooling treatments were administered. After 14 h, the patient again developed chills that lasted for approximately 20 min, accompanied by uterine contractions and membrane rupture. After 3 h, she had a miscarriage and rapidly developed septic shock. She was transferred to the intensive care unit for further infection control, shock correction, and circulatory stabilization. The cultures of blood, secretion specimen, and amniotic fluid indicated infection using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, an advanced tool for bacterial species identification.
CONCLUSIONS
is an opportunistic pathogen in pregnant women. Poor physical conditions and pregnancy may accelerate disease progression and lead to severe inflammation.
Topics: Adult; Anti-Bacterial Agents; Chills; Female; Firmicutes; Gram-Positive Cocci; Humans; Pregnancy; Pregnant Women
PubMed: 35481409
DOI: 10.1080/03007995.2022.2072091 -
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