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Microbiology Spectrum Feb 2022Three difficult-to-cultivate, strictly anaerobic strains, AN20, AN421, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens....
Three difficult-to-cultivate, strictly anaerobic strains, AN20, AN421, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20, AN421, and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family . Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343, Phocaeicola abscessus CCUG 55929, and Capsularis zoogleoformans ATCC 33285 showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C, anteiso-C, C, C, and iso-C 3OH as the major fatty acids for all three strains and additionally C 3OH for AN421 and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20 and MK-5 plus MK-10 in strains AN421 and AN502. Strains AN421 and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of genes (, , and ) in close proximity. Interestingly, strain AN20 was found to harbor two copies of gene with >95% similarity to of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family , for which the names sp. nov. (AN20 = CCM 9041 = DSM 111154) and sp. nov. (AN421= CCM 9040 = DSM 111155) are proposed. This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by spp., spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Bacterial Typing Techniques; Bacteroidaceae; Bacteroides fragilis; Cecum; Chickens; Drug Resistance, Bacterial; Drug Resistance, Microbial; Phylogeny; RNA, Ribosomal, 16S
PubMed: 35170999
DOI: 10.1128/spectrum.01954-21 -
Glycobiology Jun 2021The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these...
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
Topics: Bacteroides; Bacteroides thetaiotaomicron; Bacteroidetes; Glycosaminoglycans; Heparitin Sulfate; Humans; Polysaccharides
PubMed: 32518945
DOI: 10.1093/glycob/cwaa054 -
The Journal of Endocrinology Feb 2017The enzyme 11β-hydroxysteroid dehydrogenase (11β-HSD) interconverts active glucocorticoids and their intrinsically inert 11-keto forms. The type 1 isozyme, 11β-HSD1,...
The enzyme 11β-hydroxysteroid dehydrogenase (11β-HSD) interconverts active glucocorticoids and their intrinsically inert 11-keto forms. The type 1 isozyme, 11β-HSD1, predominantly reactivates glucocorticoids in vivo and can also metabolise bile acids. 11β-HSD1-deficient mice show altered inflammatory responses and are protected against the adverse metabolic effects of a high-fat diet. However, the impact of 11β-HSD1 on the composition of the gut microbiome has not previously been investigated. We used high-throughput 16S rDNA amplicon sequencing to characterise the gut microbiome of 11β-HSD1-deficient and C57Bl/6 control mice, fed either a standard chow diet or a cholesterol- and fat-enriched 'Western' diet. 11β-HSD1 deficiency significantly altered the composition of the gut microbiome, and did so in a diet-specific manner. On a Western diet, 11β-HSD1 deficiency increased the relative abundance of the family Bacteroidaceae, and on a chow diet, it altered relative abundance of the family Prevotellaceae Our results demonstrate that (i) genetic effects on host-microbiome interactions can depend upon diet and (ii) that alterations in the composition of the gut microbiome may contribute to the aspects of the metabolic and/or inflammatory phenotype observed with 11β-HSD1 deficiency.
Topics: 11-beta-Hydroxysteroid Dehydrogenase Type 1; Animals; Bacteroidaceae; Cecum; Colon; Diet, Western; Gastrointestinal Microbiome; Mice; Mice, Knockout
PubMed: 27885053
DOI: 10.1530/JOE-16-0578 -
International Journal of Molecular... Apr 2024(Pg) and its gingipain proteases contribute to Alzheimer's disease (AD) pathogenesis through yet unclear mechanisms. Cellular secretion of small extracellular vesicles...
(Pg) and its gingipain proteases contribute to Alzheimer's disease (AD) pathogenesis through yet unclear mechanisms. Cellular secretion of small extracellular vesicles or exosomes (EXO) increases with aging as part of the senescence-associated secretory phenotype (SASP). We have shown that EXO isolated from Pg-infected dendritic cells contain gingipains and other Pg antigens and transmit senescence to bystander gingival cells, inducing alveolar bone loss in mice in vivo. Here, EXO were isolated from the gingiva of mice and humans with/without periodontitis (PD) to determine their ability to penetrate the blood-brain barrier (BBB) in vitro and in vivo. PD was induced by Pg oral gavage for 6 weeks in C57B6 mice. EXO isolated from the gingiva or brain of donor Pg-infected (PD EXO) or control animals (Con EXO) were characterized by NTA, Western blot, and TEM. Gingival PD EXO or Con EXO were labeled and injected into the gingiva of uninfected WT mouse model. EXO biodistribution in brains was tracked by an in vivo imaging system (IVIS) and confocal microscopy. The effect of human PD EXO on BBB integrity and permeability was examined using TEER and FITC dextran assays in a human in vitro 3D model of the BBB. Pg antigens (RGP and Mfa-1) were detected in EXO derived from gingival and brain tissues of donor Pg-infected mice. Orally injected PD EXO from donor mice penetrated the brains of recipient uninfected mice and colocalized with hippocampal microglial cells. IL-1β and IL-6 were expressed in human PD EXO and not in Con EXO. Human PD EXO promoted BBB permeability and penetrated the BBB in vitro. This is the first demonstration that microbial-induced EXO in the oral cavity can disseminate, cross the BBB, and may contribute to AD pathogenesis.
Topics: Blood-Brain Barrier; Animals; Humans; Mice; Extracellular Vesicles; Porphyromonas gingivalis; Periodontitis; Gingiva; Mice, Inbred C57BL; Male; Exosomes; Female; Bacteroidaceae Infections
PubMed: 38674094
DOI: 10.3390/ijms25084509 -
Journal of Lipid Research Jun 2017In addition to functioning as detergents that aid digestion of dietary lipids in the intestine, some bile acids have been shown to exhibit antimicrobial activity....
In addition to functioning as detergents that aid digestion of dietary lipids in the intestine, some bile acids have been shown to exhibit antimicrobial activity. However, detailed information on the bactericidal activities of the diverse molecular species of bile acid in humans and rodents is largely unknown. Here, we investigated the toxicity of 14 typical human and rodent free bile acids (FBAs) by monitoring intracellular pH, membrane integrity, and viability of a human intestinal bacterium, Japan Collection of Microorganisms (JCM) 1192, upon exposure to these FBAs. Of all FBAs evaluated, deoxycholic acid (DCA) and chenodeoxycholic acid displayed the highest toxicities. Nine FBAs common to humans and rodents demonstrated that α-hydroxy-type bile acids are more toxic than their oxo-derivatives and β-hydroxy-type epimers. In five rodent-specific FBAs, β-muricholic acid and hyodeoxycholic acid showed comparable toxicities at a level close to DCA. Similar trends were observed for the membrane-damaging effects and bactericidal activities to JCM 1395 and DSM 2079, commonly represented in the human and rodent gut microbiota. These findings will help us to determine the fundamental properties of FBAs and better understand the role of FBAs in the regulation of gut microbiota composition.
Topics: Animals; Anti-Bacterial Agents; Bacteroidaceae; Bifidobacterium breve; Bile Acids and Salts; Cell Membrane; Humans; Hydrogen-Ion Concentration; Hydrophobic and Hydrophilic Interactions; Intestine, Large; Intracellular Space; Mice; Microbial Viability
PubMed: 28404640
DOI: 10.1194/jlr.M075143 -
Hua Xi Kou Qiang Yi Xue Za Zhi = Huaxi... Aug 2016Chronic periodontitis is one of the most common oral diseases in humans, the main recognized pathogenic bac-terium of which is the Porphyromonas gingivalis. Various... (Review)
Review
Chronic periodontitis is one of the most common oral diseases in humans, the main recognized pathogenic bac-terium of which is the Porphyromonas gingivalis. Various types of viruses have been detected in periodontal disease in situ, and the joint action of viral and bacterial pathogens infection mechanism are complicated. Porphyromonas gingivalis has the characteristics resulting from the interaction with a variety of bacterium viruses, which may be the reason for chronic perio-dontitis being a protracted disease associated with a variety of systemic diseases. In this paper, we reviewed the relationship between Porphyromonas gingivalis and viral diseases to provide a new idea for the treatment of patients with periodontal disease and viral infections.
Topics: Bacteroidaceae Infections; Humans; Porphyromonas gingivalis; Virus Diseases
PubMed: 28317365
DOI: 10.7518/hxkq.2016.04.021 -
The Keio Journal of Medicine Sep 2003Porphyromonas gingivalis (P. gingivalis), a gram-negative anaerobe, is involved in the pathogenesis of periodontal disease, and is found frequently in the subgingival... (Review)
Review
Porphyromonas gingivalis (P. gingivalis), a gram-negative anaerobe, is involved in the pathogenesis of periodontal disease, and is found frequently in the subgingival flora in patients with periodontitis. This organism possesses a variety of virulence factors including lipopolysaccharide, capsular material, fimbriae and proteases (enzymes). Among the P. gingivalis antigens, enzymes such as Arginine-specific gingipains (RgpA, RgpB) and lysine-specific gingipain (Kgp) have been studied for their ability to induce biologically significant antibodies. This review summarizes recent information on the gingipains and their possible application in the development of an anti-P. gingivalis vaccine.
Topics: Adhesins, Bacterial; Animals; Antigens; Bacteroidaceae Infections; Cysteine Endopeptidases; Gingipain Cysteine Endopeptidases; Hemagglutinins; Humans; Phagocytosis; Porphyromonas gingivalis; Protein Structure, Tertiary; Vaccines; Virulence Factors
PubMed: 14529148
DOI: 10.2302/kjm.52.158 -
Proceedings of the National Academy of... Jan 2022Bacterial behavior and virulence during human infection is difficult to study and largely unknown, as our vast knowledge of infection microbiology is primarily derived...
Bacterial behavior and virulence during human infection is difficult to study and largely unknown, as our vast knowledge of infection microbiology is primarily derived from studies using in vitro and animal models. Here, we characterize the physiology of , a periodontal pathogen, in its native environment using 93 published metatranscriptomic datasets from periodontally healthy and diseased individuals. transcripts were more abundant in samples from periodontally diseased patients but only above 0.1% relative abundance in one-third of diseased samples. During human infection, highly expressed genes encoding virulence factors such as fimbriae and gingipains (proteases) and genes involved in growth and metabolism, indicating that is actively growing during disease. A quantitative framework for assessing the accuracy of model systems showed that 96% of genes were expressed similarly in periodontitis and in vitro midlogarithmic growth, while significantly fewer genes were expressed similarly in periodontitis and in vitro stationary phase cultures (72%) or in a murine abscess infection model (85%). This high conservation in gene expression between periodontitis and logarithmic laboratory growth is driven by overall low variance in gene expression, relative to other pathogens including and Together, this study presents strong evidence for the use of simple test tube growth as the gold standard model for studying biology, providing biological relevance for the thousands of laboratory experiments performed with logarithmic phase Furthermore, this work highlights the need to quantitatively assess the accuracy of model systems.
Topics: Animals; Bacteroidaceae Infections; Fimbriae, Bacterial; Gingipain Cysteine Endopeptidases; Humans; Laboratories; Mice; Periodontitis; Porphyromonas gingivalis; Transcriptome; Virulence; Virulence Factors
PubMed: 34992142
DOI: 10.1073/pnas.2116637119 -
A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema.Gut Microbes Nov 2020Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used...
Evidence is accumulating that the establishment of the gut microbiome in early life influences the development of atopic eczema. In this longitudinal study, we used integrated multi-omics analyses to infer functional mechanisms by which the microbiome modulates atopic eczema risk. We measured the functionality of the gut microbiome and metabolome of 63 infants between ages 3 weeks and 12 months with well-defined eczema cases and controls in a sub-cohort from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) mother-offspring cohort. At 3 weeks, the microbiome and metabolome of allergen-sensitized atopic eczema infants were characterized by an enrichment of and , associated with increased stool D-glucose concentration and increased gene expression of associated virulence factors. A delayed colonization by beneficial and subsequent delayed accumulation of butyrate and propionate producers after 3 months was also observed. Here, we describe an aberrant developmental trajectory of the gut microbiome and stool metabolome in allergen sensitized atopic eczema infants. The infographic describes an impaired developmental trajectory of the gut microbiome and metabolome in allergen-sensitized atopic eczema (AE) infants and infer its contribution in modulating allergy risk in the Singaporean mother-offspring GUSTO cohort. The key microbial signature of AE is characterized by (1) an enrichment of and which are associated with accumulation of pre-glycolysis intermediates (D-glucose) via the trehalose metabolic pathway, increased gene expression of associated virulence factors (invasin, adhesin, flagellin and lipopolysaccharides) by utilizing ATP from oxidative phosphorylation and delayed production of butyrate and propionate, (2) depletion of which resulted in lower expression of immunostimulatory bacterial cell envelope structure and folate (vitamin B9) biosynthesis pathway, and (3) accompanied depletion of bacterial groups with the ability to derive butyrate and propionate through direct or indirect pathways which collectively resulted in reduced glycolysis, butyrate and propionate biosynthesis.
Topics: Allergens; Bacteroidaceae; Butyrates; Carbohydrate Metabolism; Dermatitis, Atopic; Enterobacteriaceae; Fatty Acids, Volatile; Feces; Female; Gastrointestinal Microbiome; Gastrointestinal Tract; Glucose; Glycolysis; Humans; Infant; Infant, Newborn; Longitudinal Studies; Male; Metabolome; Propionates; Transcriptome; Virulence Factors
PubMed: 33023370
DOI: 10.1080/19490976.2020.1801964 -
Microbiological Reviews Mar 1979
Review
Topics: Animals; Antibodies, Bacterial; Antigens, Bacterial; Antigens, Surface; Bacterial Proteins; Bacterial Vaccines; Bacteroidaceae; Bacteroides; Bacteroides Infections; Fusobacterium; Humans; Immunity, Cellular; Lipopolysaccharides; Serotyping
PubMed: 379575
DOI: 10.1128/mr.43.1.103-115.1979