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Microbiome Feb 2021The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit...
BACKGROUND
The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.
RESULTS
In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.
CONCLUSIONS
The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.
Topics: Adult; Aged; Anti-Bacterial Agents; China; Drug Resistance, Microbial; Ethnicity; Female; Genes, Bacterial; Humans; Male; Metagenomics; Microbiota; Middle Aged; Moraxella; North America; Propionibacteriaceae; Skin; Staphylococcus; Symbiosis; Young Adult
PubMed: 33597039
DOI: 10.1186/s40168-020-00995-7 -
Journal of Bacteriology Jul 1946
Topics: Bacteria; Corynebacterium; Propionibacterium acnes
PubMed: 20994865
DOI: 10.1128/JB.52.1.15-23.1946 -
International Journal of Systematic and... Sep 2007Four Gram-positive, catalase-positive, short rod- or coccoid-shaped bacterial strains, R27(T), R44, R45 and R47, were isolated from an enrichment culture with diesel...
Four Gram-positive, catalase-positive, short rod- or coccoid-shaped bacterial strains, R27(T), R44, R45 and R47, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains R27(T), R44, R45 and R47 belong to the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains form a distinct evolutionary lineage within the family Propionibacteriaceae. The novel four strains had cell-wall peptidoglycan based on LL-diaminopimelic acid, MK-9(H(4)) as the predominant menaquinone and anteiso-C(15 : 0) as the major cellular fatty acid. The DNA G+C contents were 68.8-69.2 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the four novel strains from recognized members of the family Propionibacteriaceae. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strains R27(T), R44, R45 and R47 are classified as representatives of a new genus and novel species, Aestuariimicrobium kwangyangense gen. nov., sp. nov., within the family Propionibacteriaceae. The type strain of Aestuariimicrobium kwangyangense sp. nov. is R27(T) (=KCTC 19182(T)=JCM 14204(T)).
Topics: Bacterial Typing Techniques; Base Composition; Catalase; Cell Wall; DNA, Bacterial; DNA, Ribosomal; Diaminopimelic Acid; Fatty Acids; Gasoline; Genes, rRNA; Geologic Sediments; Hydrocarbons; Korea; Molecular Sequence Data; Peptidoglycan; Phylogeny; Propionibacteriaceae; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Vitamin K 2
PubMed: 17766882
DOI: 10.1099/ijs.0.64917-0 -
Enfermedades Infecciosas Y... 2021It has been reported that microbiological diagnosis of Cutibacterium spp. infection requires a prolonged incubation time (up to 14 days). We present our experience with...
INTRODUCTION
It has been reported that microbiological diagnosis of Cutibacterium spp. infection requires a prolonged incubation time (up to 14 days). We present our experience with regard to incubation time for detection of Cutibacterium spp. in orthopaedic samples over a 10-year period.
METHODS
One hundred and nineteen samples were included in this retrospective study. Fifty-three were implants (having previously undergone sonication), 64 were periprosthetic tissue biopsies and two were synovial fluids. Atkins's criteria were used for interpreting the isolates. Quantification and number of days until a culture became positive for Cutibacterium spp. were evaluated.
RESULTS
The median number of days to detection of a clinically significant isolate and a contaminant was 4 days. No clinically significant isolates grew after day eight.
CONCLUSION
Most clinically significant isolates of Cutibacterium spp. are detected in the first 7 days of incubation, although a recommendation of prolonged incubation (up to 14 days) appears to be necessary for detecting other organisms.
Topics: Humans; Orthopedics; Propionibacteriaceae; Prosthesis-Related Infections; Retrospective Studies; Sonication
PubMed: 34088450
DOI: 10.1016/j.eimce.2020.05.017 -
Anaerobe Aug 2015The main topic of this paper is the evaluation of adhesion of propionibacteria to IPEC-J2 cells and the survival at pH 2.5 and with 0.3% bile salts added, bioactivity...
The main topic of this paper is the evaluation of adhesion of propionibacteria to IPEC-J2 cells and the survival at pH 2.5 and with 0.3% bile salts added, bioactivity towards pathogens and antibiotic resistance of Propionibacterium freudenreichii subsp. shermanii, Propionibacterium jensenii, Propionibacterium acidipropionici and Propionibacterium thoenii. Adhesion to IPEC-J2 cell lines was ca. 25-35% and significantly increased with CaCl2. Moreover, propionibacteria showed a reduction of cell count of ca. 0.5% at pH 2.5 after 3 h, whereas cell count increased after 24 h with bile salts; finally, they significantly inhibited Escherichia coli O157:H7.
Topics: Animals; Antibiosis; Bacterial Adhesion; Bile Acids and Salts; Cell Line; Drug Resistance, Bacterial; Epithelial Cells; Hydrogen-Ion Concentration; Microbial Viability; Probiotics; Propionibacterium; Swine
PubMed: 26079323
DOI: 10.1016/j.anaerobe.2015.06.003 -
Journal of the American Academy of... Sep 2019
Comparative Study
Topics: Acne Vulgaris; Adolescent; Adult; Age Factors; Anti-Bacterial Agents; Bacterial Typing Techniques; Child; Drug Resistance, Bacterial; Female; Humans; Microbial Sensitivity Tests; Middle Aged; Propionibacterium acnes; Prospective Studies; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Young Adult
PubMed: 30905801
DOI: 10.1016/j.jaad.2019.03.040 -
Brazilian Journal of Biology = Revista... 2022The gastrointestinal microflora regulates the body's functions and plays an important role in its health. Dysbiosis leads to a number of chronic diseases such as...
The gastrointestinal microflora regulates the body's functions and plays an important role in its health. Dysbiosis leads to a number of chronic diseases such as diabetes, obesity, inflammation, atherosclerosis, etc. However, these diseases can be prevented by using probiotics - living microorganisms that benefit the microflora and, therefore, improve the host organism's health. The most common probiotics include lactic acid bacteria of the Bifidobacterium and Propionibacterium genera. We studied the probiotic properties of the following strains: Bifidobacterium adolescentis АС-1909, Bifidobacterium longum infantis АС-1912, Propionibacterium jensenii В-6085, Propionibacterium freudenreichii В-11921, Propionibacterium thoenii В-6082, and Propionibacterium acidipropionici В-5723. Antimicrobial activity was determined by the 'agar blocks' method against the following test cultures: Escherichia coli ATCC 25922, Salmonella enterica ATCC 14028, Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa B6643, Proteus vulgaris ATCC 63, and Listeria monocytogenes ATCC 7644. Moderate antimicrobial activity against all the test cultures was registered in Bifidobacterium adolescentis АС-1909, Propionibacterium jensenii В-6085, and Propionibacterium thoenii В-6082. Antioxidant activity was determined by the DPPH inhibition method in all the lactic acid strains. Our study indicated that some Propionibacterium and Bifidobacterium strains or, theoretically, their consortia could be used as probiotic cultures in dietary supplements or functional foods to prevent a number of chronic diseases.
Topics: Anti-Infective Agents; Bifidobacterium; Escherichia coli; Gastrointestinal Tract; Probiotics; Propionibacteriaceae; Propionibacterium
PubMed: 35544788
DOI: 10.1590/1519-6984.256945 -
Applied and Environmental Microbiology Jun 2021Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are...
Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.
Topics: Acetates; Acetyl Coenzyme A; Adenosine Triphosphate; Coenzyme A-Transferases; Fermentation; Genome, Bacterial; Propionibacteriaceae; Succinate-CoA Ligases
PubMed: 33931420
DOI: 10.1128/AEM.02959-20 -
Environmental Microbiology Jun 2021In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium...
In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium jensenii, Acidipropionibacterium thoenii and Propionibacterium freudenreichii) when exposed to oxygen, implicating functional respiratory systems. Using an optimal microaerobic condition, P. freudenreichii DSM 20271 consumed lactate to produce propionate and acetate initially. When lactate was depleted propionate was oxidized to acetate. We propose to name the switch from propionate production to consumption in microaerobic conditions the 'propionate switch'. When propionate was depleted the 'acetate switch' occurred, resulting in complete consumption of acetate. Both growth rate on lactate (0.100 versus 0.078 h ) and biomass yield (20.5 versus 8.6 g* mol lactate) increased compared to anaerobic conditions. Proteome analysis revealed that the abundance of proteins involved in the aerobic and anaerobic electron transport chains and major metabolic pathways did not significantly differ between anaerobic and microaerobic conditions. This implicates that P. freudenreichii is prepared for utilizing O when it comes available in anaerobic conditions. The ecological niche of propionic acid bacteria can conceivably be extended to environments with oxygen gradients from oxic to anoxic, so-called microoxic environments, as found in the rumen, gut and soils, where they can thrive by utilizing low concentrations of oxygen.
Topics: Carbon Dioxide; Lactic Acid; Propionates; Propionibacteriaceae; Propionibacterium freudenreichii
PubMed: 33955639
DOI: 10.1111/1462-2920.15532 -
Applied and Environmental Microbiology Nov 1989Propionibacterium acnes P13 was isolated from human feces. The bacterium produced a particulate nitrate reductase and a soluble nitrite reductase when grown with nitrate...
Propionibacterium acnes P13 was isolated from human feces. The bacterium produced a particulate nitrate reductase and a soluble nitrite reductase when grown with nitrate or nitrite. Reduced viologen dyes were the preferred electron donors for both enzymes. Nitrous oxide reductase was never detected. Specific growth rates were increased by nitrate during growth in batch culture. Culture pH strongly influenced the products of dissimilatory nitrate reduction. Nitrate was principally converted to nitrite at alkaline pH, whereas nitrous oxide was the major product of nitrate reduction when the bacteria were grown at pH 6.0. Growth yields were increased by nitrate in electron acceptor-limited chemostats, where nitrate was reduced to nitrite, showing that dissimilatory nitrate reduction was an energetically favorable process in P. acnes. Nitrate had little effect on the amounts of fermentation products formed, but molar ratios of acetate to propionate were higher in the nitrate chemostats. Low concentrations of nitrite (ca. 0.2 mM) inhibited growth of P. acnes in batch culture. The nitrite was slowly reduced to nitrous oxide, enabling growth to occur, suggesting that denitrification functions as a detoxification mechanism.
Topics: Feces; Humans; Hydrogen-Ion Concentration; Nitrate Reductases; Nitrates; Nitrite Reductases; Nitrites; Nitrous Oxide; Propionibacterium acnes
PubMed: 2624464
DOI: 10.1128/aem.55.11.2899-2903.1989