TL;DR: It is shown that conjugal gene transfer has made a major contribution to increased antibiotic resistance in Bacteroides species, a numerically predominant group of human colonic bacteria, and the hypothesis that extensive gene transfer occurs among bacteria in the human colon, both within the genus Bactoides and among Bactoeides species and gram-positive bacteria.
Abstract: Transfer of antibiotic resistance genes by conjugation is thought to play an important role in the spread of resistance. Yet virtually no information is available about the extent to which such horizontal transfers occur in natural settings. In this paper, we show that conjugal gene transfer has made a major contribution to increased antibiotic resistance in Bacteroides species, a numerically predominant group of human colonic bacteria. Over the past 3 decades, carriage of the tetracycline resistance gene, tetQ, has increased from about 30% to more than 80% of strains. Alleles of tetQ in different Bacteroides species, with one exception, were 96 to 100% identical at the DNA sequence level, as expected if horizontal gene transfer was responsible for their spread. Southern blot analyses showed further that transfer of tetQ was mediated by a conjugative transposon (CTn) of the CTnDOT type. Carriage of two erythromycin resistance genes, ermF and ermG, rose from <2 to 23% and accounted for about 70% of the total erythromycin resistances observed. Carriage of tetQ and the erm genes was the same in isolates taken from healthy people with no recent history of antibiotic use as in isolates obtained from patients with Bacteroides infections. This finding indicates that resistance transfer is occurring in the community and not just in clinical environments. The high percentage of strains that are carrying these resistance genes in people who are not taking antibiotics is consistent with the hypothesis that once acquired, these resistance genes are stably maintained in the absence of antibiotic selection. Six recently isolated strains carried ermB genes. Two were identical to erm(B)-P from Clostridium perfringens, and the other four had only one to three mismatches. The nine strains with ermG genes had DNA sequences that were more than 99% identical to the ermG of Bacillus sphaericus. Evidently, there is a genetic conduit open between gram-positive bacteria, including bacteria that only pass through the human colon, and the gram-negative Bacteroides species. Our results support the hypothesis that extensive gene transfer occurs among bacteria in the human colon, both within the genus Bacteroides and among Bacteroides species and gram-positive bacteria.
TL;DR: The moderately saccharolytic, predominantly oral Bacteroides species, which include B. melaninogenicus, B. oralis, and related species, form a phenotypically and phylogenetically coherent group of species which differ so significantly from the emended description of the genus Bactroides that they should not be classified in the same genus.
Abstract: It was recently proposed that the genus Bacteroides should be restricted to Bacteroides fragilis (the type species) and closely related organisms (viz., B. caccae, B. distasonis, B. eggerthii, B. merdae, B. ovatus, B. stercoris, B. thetaiotaomicron, B. uniformis, and B. vulgatus). By contrast, the moderately saccharolytic, predominantly oral Bacteroides species, which include B. melaninogenicus, B. oralis, and related species, form a phenotypically and phylogenetically coherent group of species which differ so significantly from the emended description of the genus Bacteroides that they should not be classified in the same genus. Therefore, we formally propose that these species be reclassified in a new genus, Prevotella. The type species is Prevotella melaninogenica.
TL;DR: The gut microbiota is established during infancy and plays a fundamental role in shaping host immunity, and Colonization patterns may influence the development of atopic disease, but existing evidence is limited and conflicting.
Abstract: Background The gut microbiota is established during infancy and plays a fundamental role in shaping host immunity. Colonization patterns may influence the development of atopic disease, but existing evidence is limited and conflicting. Objective To explore associations of infant gut microbiota and food sensitization. Methods Food sensitization at 1 year was determined by skin prick testing in 166 infants from the population-based Canadian Healthy Infant Longitudinal Development (CHILD) study. Faecal samples were collected at 3 and 12 months, and microbiota was characterized by Illumina 16S rRNA sequencing. Results Twelve infants (7.2%) were sensitized to ≥ 1 common food allergen at 1 year. Enterobacteriaceae were overrepresented and Bacteroidaceae were underrepresented in the gut microbiota of food-sensitized infants at 3 months and 1 year, whereas lower microbiota richness was evident only at 3 months. Each quartile increase in richness at 3 months was associated with a 55% reduction in risk for food sensitization by 1 year (adjusted odds ratio 0.45, 95% confidence interval 0.23-0.87). Independently, each quartile increase in Enterobacteriaceae/Bacteroidaceae ratio was associated with a twofold increase in risk (2.02, 1.07-3.80). These associations were upheld in a sensitivity analysis among infants who were vaginally delivered, exclusively breastfed and unexposed to antibiotics. At 1 year, the Enterobacteriaceae/Bacteroidaceae ratio remained elevated among sensitized infants, who also tended to have decreased abundance of Ruminococcaceae. Conclusions and clinical relevance Low gut microbiota richness and an elevated Enterobacteriaceae/Bacteroidaceae ratio in early infancy are associated with subsequent food sensitization, suggesting that early gut colonization may contribute to the development of atopic disease, including food allergy.
TL;DR: It is proposed that Bacteroides asaccharolyticus (Holdeman and Moore) Finegold and Barnes, Bactseroides gingivalis Coykendall, Kaczmarek and Slots, and Bactroides endodontalis van Steenbergen, van Winkelhoff, Mayrand, Grenier and de Graaff be reclassified in a new genus, Porphyromonas, as Porphyromeonas asac charoly
Abstract: The asaccharolytic, pigmented Bacteroides, Bacteroides asaccharolyticus, Bacteroides gingivalis, and Bacteroides endodontalis, form a group of relatively homogeneous species which differ markedly in biochemical and chemical properties from the type species of Bacteroides, Bacteroides fragilis (Castellani and Chalmers), such that they should not be retained within this genus. Therefore, we propose that Bacteroides asaccharolyticus (Holdeman and Moore) Finegold and Barnes, Bacteroides gingivalis Coykendall, Kaczmarek and Slots, and Bacteroides endodontalis van Steenbergen, van Winkelhoff, Mayrand, Grenier and de Graaff be reclassified in a new genus, Porphyromonas, as Porphyromonas asaccharolytica comb. nov., Porphyromonas gingivalis comb. nov., and Porphyromonas endodontalis comb. nov., respectively.
TL;DR: It was found that there is a close relationship between the amounts of vitamin B 12 and viable counts of Bacteroides type A in the intestinal contents of carp, and this results strongly suggested that the Bacternes type A is closely involved in vitamin B12 production in the intestine tract of freshwater fish.