-
Clinical Infectious Diseases : An... Sep 1997A new method of identifying bacteria, phylogenetic 16S rRNA sequencing, has led to major reorganizations among most genera of anaerobic bacteria. The pigmented... (Review)
Review
A new method of identifying bacteria, phylogenetic 16S rRNA sequencing, has led to major reorganizations among most genera of anaerobic bacteria. The pigmented Prevotella species now comprise seven species including P. nigrescens and P. tannerae; P. intermedia/P. nigrescens-like organisms await inclusion. The former Mitsuokella dentalis and Hallella seregens were transferred to Prevotella as one species, P. dentalis. P. enoeca is a new nonpigmenting Prevotella. The genus Porphyromonas currently includes 11 pigmented species and one nonpigmented species, P. catoniae; P. levii-like and P. endodontalis-like organisms are candidates for the genus. Fusobacterium nucleatum currently has five subspecies, and F. varium includes the former F. pseudonecrophorum. Former Wolinella recta and Wolinella curva now are Campylobacter rectus and Campylobacter curvus; Campylobacter showae is a new species. Isolates included in the bile-sensitive former Bacteroides gracilis now are Campylobacter gracilis; the bile-resistant B. gracilis isolates were transferred to a new genus, Sutterella, as S. wadsworthensis. The new Actinomyces species include two subspecies of the A. neuii and the A. radingae-A. turicensis complex. The genus Eubacterium sensu stricto is represented by E. limosum, and the former E. alactolyticum was reclassified in a new genus, Pseudoramibacter, as P. alactolyticus. Recent entries include E. saphenum, E. minutum, E. exiguum, E. infirmum, and E. tardum. A new genus, Atopobium houses some former lactobacilli and streptococci. The genus Peptostreptococcus also have four new species; P. hydrogenalis, P. lacrimalis, P. lactolyticus, and P. vaginalis.
Topics: Bacteria, Anaerobic; Gram-Negative Anaerobic Bacteria; Gram-Positive Bacteria; Humans
PubMed: 9310640
DOI: 10.1086/516227 -
MSystems Aug 2021Bovine digital dermatitis (DD) is a skin disorder that is a significant cause of infectious lameness in cattle around the world. However, very little is known about the...
Bovine digital dermatitis (DD) is a skin disorder that is a significant cause of infectious lameness in cattle around the world. However, very little is known about the etiopathogenesis of the disease and the microbiota associated with DD in beef cattle. In this study, we provide a comprehensive characterization of DD and healthy skin microbiota of feedlot beef cattle. We also developed and validated a novel multiplex quantitative PCR (qPCR) assay to quantify the distribution of DD-associated bacterial species across DD lesion stages. We determined the DD-associated microbiota with deep amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene, followed by the application of novel and existing qPCR assays to quantify species distributions of Treponema, , , and across lesion stages. Deep amplicon sequencing revealed that Treponema, , , and were associated with DD lesions. Culturing of DD biopsy specimens identified Porphyromonas levii, Bacteroides pyogenes, and two spp. within DD lesions. Using species-specific qPCR on DD lesion DNA, we identified P. levii in 100% of active lesion stages. Early-stage lesions were particularly associated with Treponema medium, T. phagedenis, and . This study suggests a core DD microbial group consisting of species of Treponema, , , and , which may be closely tied with the etiopathogenesis of DD. Further characterizations of these species and spp. are necessary to understand the microbial factors involved in DD pathogenesis, which will help elucidate DD etiology and facilitate more targeted and effective mitigation and treatment strategies. Previous work, primarily in dairy cattle, has identified various taxa associated with digital dermatitis (DD) lesions. However, there is a significant gap in our knowledge of DD microbiology in beef cattle. In addition, characterization of bacteria at the species level in DD lesions is limited. In this study, we provide a framework for the accurate and reproducible quantification of major DD-associated bacterial species from DNA samples. Our findings support DD as a polymicrobial infection, and we identified a variety of bacterial species spanning multiple genera that are consistently associated with DD lesions. The DD-associated microbiota identified in this study may be capable of inducing the formation and progression of DD lesions and thus should be primary targets in future DD pathogenesis studies.
PubMed: 34313462
DOI: 10.1128/mSystems.00708-21 -
Animals : An Open Access Journal From... Dec 2022The aim of the study was to characterize the dynamics of anaerobic cultivable postpartum microbiota in the uterus of dairy cows. In total, 122 dairy cows were enrolled...
The aim of the study was to characterize the dynamics of anaerobic cultivable postpartum microbiota in the uterus of dairy cows. In total, 122 dairy cows were enrolled and sampled on day 0 (day of calving) and on days 3, 9, 15, 21, and 28 postpartum (pp). Samples were cultivated anaerobically and analyzed by MALDI-TOF MS. In total, 1858 isolates were recovered. The most prevalent facultative anaerobic genera were (27.8%), (25.4%), and (13.1%). The most prevalent obligate anaerobes were (9.3%), (3.3%), and (2.4%). The microbial communities were highly dynamic and diverse. On the animal level, on day 21 and 28 pp was associated with clinical endometritis, and on day 21 pp was associated with subclinical endometritis. The occurrence of on day 28 was related to uterine health. The presence of , , and was significantly associated with an increased risk for purulent vaginal discharge. Primiparous cows showed a higher prevalence of , , , and spp. than multiparous cows but were not more susceptible to uterine diseases. This study might provide a suitable basis for future co-cultivation studies to elucidate potential synergistic interactions between microbiota.
PubMed: 36611691
DOI: 10.3390/ani13010082 -
Frontiers in Veterinary Science 2022Interdigital hyperplasia (IH) is a fold of fibrous tissue protruding into the interdigital space that rarely occurs in sheep. Interdigital hyperplasia secondary infected...
Interdigital hyperplasia (IH) is a fold of fibrous tissue protruding into the interdigital space that rarely occurs in sheep. Interdigital hyperplasia secondary infected with bovine digital dermatitis (BDD) treponemes has been reported in cattle in the course of the increasing spread of classical BDD lesions. In this report, we describe proliferative/ulcerative interdigital lesions associated with contagious ovine digital dermatitis (CODD) treponemes and clinically scored as (IH+CODD), occurring in both hind limbs of a ram and the left hindlimb of a ewe. Both cases exhibited epidermal hyperplasia, parakeratosis and focal-extensive areas of epidermal necrosis with numerous infiltrating neutrophils. PCR and fluorescence hybridization (FISH) were positive for phylotype 1 (PT1). In addition, and were detected in the biopsy by PCR. In three slaughter sheep, without claw lesions, which were kept together with both affected sheep, spp. were detected neither with PCR nor FISH; the PCRs for and were also negative. Complete clinical healing occurred in the ewe within 6 weeks after three local applications of a chlortetracycline spray in 2 weeks intervals. This report is the first description of IH+CODD in sheep as demonstrated by a combination of histopathological and molecular analyses.
PubMed: 36686194
DOI: 10.3389/fvets.2022.1028880 -
Treatment of digital dermatitis using salicylic acid in European bison () reveals promising results.Frontiers in Veterinary Science 2022Digital dermatitis (DD) associated with the presence of multiple spp. was recently described for the first time in European bison (). DD is characterized by skin...
Digital dermatitis (DD) associated with the presence of multiple spp. was recently described for the first time in European bison (). DD is characterized by skin inflammation in the distal foot area in various ungulates. The objective of this proof of concept study was to test a treatment protocol adopted from cattle for its applicability in this wildlife species using five animals. Keratolytic salicylic acid paste was administered topically under bandages for seven days to enable removal of the affected skin. All interventions were performed under general anesthesia. To evaluate the treatment efficacy, photographs and biopsies were taken pre- and post-treatment. The biopsies were examined histologically, by PCR for the presence of different bacterial species, by -specific fluorescent hybridization (FISH), and by transmission electron microscopy. Based on photographs, complete clinical healing of the 15 feet with macroscopical DD lesions was achieved. Histological examination showed mild to moderate dermatitis in 17/20 feet before, and in 12/20 feet after treatment. 17/20 feet were spp. PCR positive before, and none was positive after treatment. , and could not be detected in any of the samples. By FISH and electron microscopy, spp. could be visualized in the stratum corneum before, but not after treatment. These results suggest that this treatment method can be applied as standard practice prior to transporting DD affected European bison to prevent the spread of this contagious disease.
PubMed: 36532358
DOI: 10.3389/fvets.2022.1012226 -
Frontiers in Veterinary Science 2022The increasing prevalence of bovine digital dermatitis (BDD) contributes to a higher occurrence of secondary infections of exposed corium with spp. in bovine claws....
The increasing prevalence of bovine digital dermatitis (BDD) contributes to a higher occurrence of secondary infections of exposed corium with spp. in bovine claws. "Non-healing" claw horn lesions (NHL) clinically resemble BDD lesions. They are severe, cause chronic lameness, and may persist for several months. They poorly respond to standard treatments of BDD and represent a serious welfare issue. In this study, four cases of NHL were classified clinically either as BDD-associated axial horn fissures (BDD-HFA; = 3) or BDD-associated sole ulcer (BDD-SU; = 1). In all four cases, pronounced multifocal keratinolysis of the stratum corneum, ulceration, and severe chronic lymphoplasmacytic perivascular to interstitial dermatitis were observed. All lesional samples tested positive for spp., (.) , and (.) by PCRs. BDD-HFA lesions contained as revealed by genetic identities of 93, 99, and 100%. Treponemes in the BDD-SU lesion were 94% homologous to phylotype PT3. Fluorescent hybridization (FISH) revealed extensive epidermal infiltration by treponemes that made up > 90% of the total bacterial population in all four lesions. FISH also tested positive for and negative for in all four cases, whilst only one BDD-HFA contained . Our data point to BDD-associated treponemes and constituting potential etiological agents in the development of "non-healing" claw horn lesions in cattle.
PubMed: 36337205
DOI: 10.3389/fvets.2022.1041215 -
Infection and Immunity Sep 2016Periodontitis is a significant problem in companion animals, and yet little is known about the disease-associated microbiota. A major virulence factor for the human...
Periodontitis is a significant problem in companion animals, and yet little is known about the disease-associated microbiota. A major virulence factor for the human periodontal pathogen Porphyromonas gingivalis is the lysyl- and arginyl-specific proteolytic activity of the gingipains. We screened several Porphyromonas species isolated from companion animals-P. asaccharolytica, P. circumdentaria, P. endodontalis, P. levii, P. gulae, P. macacae, P. catoniae, and P. salivosa-for Lys- and Arg-specific proteolytic activity and compared the epithelial and macrophage responses and induction of alveolar bone resorption of the protease active species to that of Porphyromonas gingivalis Only P. gulae exhibited Lys-and Arg-specific proteolytic activity. The genes encoding the gingipains (RgpA/B and Kgp) were identified in the P. gulae strain ATCC 51700 and all publicly available 12 draft genomes of P. gulae strains. P. gulae ATCC 51700 induced levels of alveolar bone resorption in an animal model of periodontitis similar to those in P. gingivalis W50 and exhibited a higher capacity for autoaggregation and binding to oral epithelial cells with induction of apoptosis. Macrophages (RAW 264.7) were found to phagocytose P. gulae ATCC 51700 and the fimbriated P. gingivalis ATCC 33277 at similar levels. In response to P. gulae ATCC 51700, macrophages secreted higher levels of cytokines than those induced by P. gingivalis ATCC 33277 but lower than those induced by P. gingivalis W50, except for the interleukin-6 response. Our results indicate that P. gulae exhibits virulence characteristics similar to those of the human periodontal pathogen P. gingivalis and therefore may play a key role in the development of periodontitis in companion animals.
Topics: Alveolar Bone Loss; Animals; Bacteroidaceae Infections; Cell Line; Disease Models, Animal; Epithelial Cells; Female; Humans; Interleukin-6; Macrophages; Mice; Mice, Inbred BALB C; Periodontitis; Porphyromonas; Porphyromonas gingivalis; Virulence; Virulence Factors
PubMed: 27354442
DOI: 10.1128/IAI.01500-15 -
Journal of Bacteriology Feb 1994The phylogenetic structure of the bacteroides subgroup of the cytophaga-flavobacter-bacteroides (CFB) phylum was examined by 16S rRNA sequence comparative analysis.... (Comparative Study)
Comparative Study
The phylogenetic structure of the bacteroides subgroup of the cytophaga-flavobacter-bacteroides (CFB) phylum was examined by 16S rRNA sequence comparative analysis. Approximately 95% of the 16S rRNA sequence was determined for 36 representative strains of species of Prevotella, Bacteroides, and Porphyromonas and related species by a modified Sanger sequencing method. A phylogenetic tree was constructed from a corrected distance matrix by the neighbor-joining method, and the reliability of tree branching was established by bootstrap analysis. The bacteroides subgroup was divided primarily into three major phylogenetic clusters which contained most of the species examined. The first cluster, termed the prevotella cluster, was composed of 16 species of Prevotella, including P. melaninogenica, P. intermedia, P. nigrescens, and the ruminal species P. ruminicola. Two oral species, P. zoogleoformans and P. heparinolytica, which had been recently placed in the genus Prevotella, did not fall within the prevotella cluster. These two species and six species of Bacteroides, including the type species B. fragilis, formed the second cluster, termed the bacteroides cluster. The third cluster, termed the porphyromonas cluster, was divided into two subclusters. The first contained Porphyromonas gingivalis, P. endodontalis, P. asaccharolytica, P. circumdentaria, P. salivosa, [Bacteroides] levii (the brackets around genus are used to indicate that the species does not belong to the genus by the sensu stricto definition), and [Bacteroides] macacae, and the second subcluster contained [Bacteroides] forsythus and [Bacteroides] distasonis. [Bacteroides] splanchnicus fell just outside the three major clusters but still belonged within the bacteroides subgroup. With few exceptions, the 16 S rRNA data were in overall agreement with previously proposed reclassifications of species of Bacteroides, Prevotella, and Porphyromonas. Suggestions are made to accommodate those species which do not fit previous reclassification schemes.
Topics: Bacteroides; Base Sequence; DNA Primers; Molecular Sequence Data; Phylogeny; Porphyromonas; RNA, Ribosomal, 16S; Sequence Alignment; Sequence Homology, Nucleic Acid
PubMed: 8300528
DOI: 10.1128/jb.176.3.725-732.1994 -
Veterinary Microbiology Apr 2016Although treponemes are consistently identified in tissue from bovine digital dermatitis (DD) lesions, the definitive etiology of this debilitating polymicrobial disease...
Although treponemes are consistently identified in tissue from bovine digital dermatitis (DD) lesions, the definitive etiology of this debilitating polymicrobial disease is still unresolved. To study the microbiomes of 27 DD-infected and 10 healthy interdigital skin samples, we used a combination of different molecular methods. Deep sequencing of the 16S rRNA gene variable regions V1-V2 showed that Treponema, Mycoplasma, Fusobacterium and Porphyromonas were the genera best differentiating the DD samples from the controls. Additional deep sequencing analysis of the most abundant genus, Treponema, targeting another variable region of the 16S rRNA gene, V3-V4, identified 15 different phylotypes, among which Treponema phagedenis-like and Treponema refringens-like species were the most abundant. Although the presence of Treponema spp., Fusobacterium necrophorum and Porphyromonas levii was confirmed by fluorescence in situ hybridization (FISH), the results for Mycoplasma spp. were inconclusive. Extensive treponemal epidermal infiltration, constituting more than 90% of the total bacterial population, was observed in 24 of the 27 DD samples. F. necrophorum and P. levii were superficially located in the epidermal lesions and were present in only a subset of samples. RT-qPCR analysis showed that treponemes were also actively expressing a panel of virulence factors at the site of infection. Our results further support the hypothesis that species belonging to the genus Treponema are major pathogens of DD and also provide sufficient clues to motivate additional research into the role of M. fermentans, F. necrophorum and P. levii in the etiology of DD.
Topics: Animals; Biodiversity; Cattle; Cattle Diseases; Digital Dermatitis; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Microbiota; RNA, Ribosomal, 16S; Skin; Virulence Factors
PubMed: 27016768
DOI: 10.1016/j.vetmic.2016.03.003 -
Journal of Clinical Periodontology Mar 1996Detection of putative pathogens is critical for delineating the etiology and progression of periodontitis. In the present study, we have used a polymerase chain reaction...
Detection of putative pathogens is critical for delineating the etiology and progression of periodontitis. In the present study, we have used a polymerase chain reaction (PCR) assay utilizing primers specific for the lkt A gene of Actinobacillus actinomycetemcomitans, the fimbrial gene of Porphyromonas gingivalis, and tdp A gene of Treponema denticola in order to determine the presence of these pathogens in subgingival plaque samples from periodontitis sites. These gene specific primers were also used to assess the detection of different strains of bacteria in the PCR assays. Primers for P. gingivalis detected P. gingivalis strain 33277, but no product was detected when primers were used with extracts from 4 species of Capnocytophaga, 3 species of Prevotella, 2 species of Porphyromonas other than P. gingivalis, Bacteroides levii, Escherichia coli, 3 strains of A. actinomycetemcomitans and 3 strains of T. denticola. PCR analysis using primers for the lkt A gene of A. actinomycetemcomitans also did not result in a product with any of these bacteria with the exception of a positive result with 3 different strains of A. actinomycetemcomitans. Primers selected from the tdp A gene of T. denticola did not identify any of the bacteria strains tested except T. denticola serovars a, b, and c. Thus, these primers were shown to amplify gene segments that are specific to either P. gingivalis (33277), A. actinomycetemcomitans (33384, 43717 and 43718) or T. denticola (35405, 33521 and 35404). The PCR assay may be used to rapidly detect the presence of periodontal pathogens in the future.
Topics: Adolescent; Adult; Aggregatibacter actinomycetemcomitans; Bacterial Proteins; Bacteroides; Capnocytophaga; Child; Child, Preschool; DNA Primers; Dental Plaque; Disease Progression; Escherichia coli; Fimbriae, Bacterial; Genes, Bacterial; Humans; Middle Aged; Periodontitis; Polymerase Chain Reaction; Porphyromonas; Porphyromonas gingivalis; Prevotella; Serotyping; Species Specificity; Treponema
PubMed: 8707980
DOI: 10.1111/j.1600-051x.1996.tb02078.x