Allobaculum mucilyticum sp. nov. and Allobaculum fili sp. nov., isolated from the human intestinal tract.

As part of a culturomics study to identify bacterial species associated with inflammatory bowel disease, a large collection of bacteria was isolated from patients with ulcerative colitis. Two of these isolates were tentatively identified as members of the family Erysipelotrichaceae. Following phylogenetic analysis based on 16S rRNA gene sequence and genome sequences, both strain 128T and 539T were found to be most closely related to Allobaculum stercoricanis, with G+C contents of 48.6 and 50.5 mol%, respectively, and the genome sizes of 2 864 314 and 2 580 362 base pairs, respectively. Strains 128T and 539T were strict anaerobe rods that grew in long chains between 37 and 42 °C. Scanning electron microscopy did not reveal flagella, fimbriae or visible endospores. Biochemical analysis showed nearly identical results for both strains with enzymatic activity of C4 and C8 esterases, acid phosphatase, naphthol-AS-BI-phosphohydrolase, ß-glucuronidase, N-acetyl-ß-glucosaminidase and arginine arylamidase. In addition, both strains produced indole and reduced nitrate. Major fatty acids were identified as C18:1 ω9c (oleic acid, 64.06% in 128T and 74.35% in 539T), C18:1 ω7c/C18:1 ω9t/C18:1 ω12t/UN17.834 (16.18 % in 128T and 6.22% in 539T) and C16:0 (6.23% in 128T and 7.37% in 538T). Based on these analyses two novel species are proposed, Allobaculum mucilyticum sp. nov. with the type strain 128T (=NCTC 14626T=DSM 112815T) and Allobaculum fili sp. nov. with the type strain 539T (=NCTC 14627T=DSM 112814T).

Isolation and identification of a human intestinal bacterium capable of daidzein conversion.

Equol, which produced from daidzein (one of the principal isoflavones), is recognized to be the most resultful in stimulating an estrogenic and antioxidant response. The daidzein transformation was studied during fermentation of five growth media inoculated with feces from a healthy human, and a daidzein conversion strain was isolated. To enrich the bacterial population involved in daidzein metabolism in a complex mixture, fecal samples were treated with antibiotics. The improved propidium monoazide combined with the quantitative polymerase chain reaction (PMAxx-qPCR) assay showed that the ampicillin treatment of samples did result in a reduction of the total visible bacteria counts by 52.2% compared to the treatment without antibiotics. On this basis, the newly isolated rod-shaped, Gram-positive anaerobic bacterium, named strain Y11 (MN560033), was able to metabolize daidzein to equol under anaerobic conditions, with a conversion ratio (equol ratio: the amount of equol produced/amount of supplemented daizein) of 0.56 over 120 h. The 16S rRNA partial sequence of the strain Y11 exhibited 99.8% identity to that of Slackia equolifaciens strain DZE (NR116295). This study will provide new insights into the biotransformation of equol from daidzein by intestinal microbiota from the strain-level and explore the possibility of probiotic interventions.

Isachenkonia alkalipeptolytica gen. nov. sp. nov., a new anaerobic, alkaliphilic proteolytic bacterium capable of reducing Fe(III) and sulfur.

An obligately alkaliphilic, anaerobic, proteolytic bacterium was isolated from a sample of Tanatar III soda lake sediment (Altai region, Russia) and designated as strain Z-1701T. Cells of strain Z-1701T were short, straight, motile Gram-stain-positive rods. Growth of Z-1701T obligately depended on the presence of sodium carbonate. Strain Z-1701T could utilize various peptides mixtures, such as beef and yeast extracts, peptone, soytone, trypticase and tryptone, as well as such proteins as albumin, gelatin and sodium caseinate. It was able to grow oligotrophically with 0.02 g l-1 yeast extract as the sole energy and carbon source. Carbohydrates did not support the growth of strain Z-1701T. The main products released during the growth of strain Z-1701T on tryptone were formate, acetate and ammonium. Strain Z-1701T was able to reduce ferrihydrite, Fe(III)-EDTA, anthraquinone-2,6-disulfonate and elemental sulfur, using proteinaceous substrates as electron donors. In all cases the presence of the electron acceptor in the medium stimulated growth. The main cellular fatty acids were iso-C15 : 0, iso-C15 : 0 aldehyde, iso-C15 : 1 ω6, C16 : 0, iso-C17 : 0 aldehyde, C16 : 0 aldehyde and C14 : 0. The DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on the concatenated alignment of 120 protein-marker sequences revealed that strain Z-1701T falls into a cluster with the genus Tindallia, family Clostridiaceae. 16S rRNA gene sequence identity between strain Z-1701T and Tindallia species were 88.3-89.75 %. On the basis of its phenotypic characteristics and phylogenetic position, the novel isolate is considered to be a representative of a novel genus and species for which the name Isachenkonia alkalipeptolytica gen. nov., sp. nov. is proposed, with Z-1701T (=JCM 32929Т=DSM 109060Т=VKM B-3261Т) as its type strain.

Breast abscess due to Trueperella bernardiae and Actinotignum sanguinis / Absceso mamario debido a Trueperella bernardiae y Actinotignum sanguinis

No disponible

Bacteriocin-like inhibitory substance in aquaculture: a classic method of protein precipitation for a new aplicability / Substância inibidora tipo bacteriocina na aquicultura: método clássico de precipitação de proteínas para novas aplicações

Techniques to decrease losses from bacterial diseases are always important to improve the fish production. The use of antagonistic substances (bacteriocins) has been proven to be a viable option. The aim of this study was to evaluate different methods of purification for bacteriocin like inhibitory substances (BLIS). For the purification process, we isolated and used two Gram-positive bacilli that produce antagonistic substances for pathogens in aquaculture. Tests for detection of interfering factors were also performed. After the confirmation that the antagonistic action was due the BLIS activity, we carried out the purification methods. The methods tested were: cell free supernatant, acid extraction and ammonium sulfate precipitation at two concentrations (20 and 50%). Salmonella Tiphy CFP/IAL1472 and Aeromonas hydrophila (isolated in a tilapia production environment) were used as indicators of the efficiency of extracts in controlling pathogenic potentials. Ammonium sulfate precipitation at 50% was the most appropriate for purifying the antagonistic substance for both indicators. The extracts of the two isolates remained active for 22 days at 25ºC. These are promising results regarding the water and fish health without the use of antibiotics, in this manner being a safer environmental practice.

Técnicas para diminuir as perdas causadas por doenças bacterianas são importantes para melhorar continuamente a produção de pescado. O uso de substâncias antagônicas (bacteriocinas) tem-se mostrado uma opção viável. O objetivo do trabalho foi avaliar diferentes métodos de purificação de bacteriocinas como substâncias inibidoras (BLIS). Dois bacilos Gram-positivos, produtores de substâncias antagonistas para agentes patogênicos da aquicultura, foram utilizados em processos de purificação. Depois de confirmada a ação antagônica pela atividade de BLIS, os métodos de purificação foram realizados. Os métodos testados foram: células livres de sobrenadante, extração ácida e precipitação por sulfato de amônia em duas concentrações (20 e 50%). Salmonella Typhi PCP/IAL1472 e Aeromonas hydrophila (isolada de um ambiente de tilapicultura) foram utilizadas como indicadores de eficiência dos extratos. O precipitado por sulfato de amônio a 50% foi o mais adequado para purificar a substância antagonista para ambos os isolados indicadores. Os extratos dos dois isolados permaneceram ativos por 22 dias em 25ºC. Estes resultados são promissores do ponto de vista da manutenção da sanidade da água e dos peixes, sem uso de antibióticos, constituindo uma prática ambientalmente mais segura.

Flow-Diverting Stents for the Obliteration of Symptomatic, Infectious Cavernous Carotid Artery Aneurysms.

BACKGROUND: Intracavernous aneurysms constitute up to 9% of all intracranial aneurysms and 6% are infectious (IIA). First line therapy is a protracted antibiotic course, yet with failure, surgery and endovascular parent vessel sacrifice have been utilized. Reconstructive endovascular therapies have emerged for aneurysm control and may demonstrate a safer therapeutic alternative. OBJECTIVE: To present an IIA treated with a flow-diverting Pipeline stent (ev3 Neurovascular, Irvine, California). METHODS: A 41-yr-old female presented with visual loss, ophthalmoplegia, and cavernous sinus thrombosis with an associated phlegmon. Transsphenoidal evacuation was performed without complication or bleeding and she continued on medical therapy. Two weeks postoperatively, she developed a worsening right third cranial nerve palsy and MRA demonstrated a 1-cm right IIA, not evident on postoperative MRI. Three days of dual antiplatelet therapy preceded successful pipeline embolization. Angiography demonstrated aneurysm obliteration at 3 mo and her right ophthalmoplegia resolved. RESULTS: A literature review identified 6 reported cases of IIAs treated with stent embolization. Only 1 documented a flow-diverting Silk stent used in a child. All lesions were obliterated at follow-up without neurological sequelae. No complication arose with implantation in the setting of infection, and as few as 3 d of dual antiplatelet therapy was sufficient for preprocedural prophylaxis, although in Vivo antiplatelet activity may be more significant. CONCLUSION: We report the first case of an IIA treated with a flow-diverting pipeline stent. These devices preserve native vasculature and neurological function compared to surgical and endovascular vessel sacrifice strategies. They appear to be safe management options for the treatment of IIAs.

Comparación bacteriana de 30 piezas de alta velocidad antes y después de ser utilizadas en la facultad de odontología, Región Veracruz / Bacterial comparison of 30 high speed handpieces before and after being used at the school of dentistry, Veracruz Region

Introducción: en los procedimientos odontológicos se está expuestoa gran cantidad de microorganismos y las intervenciones clínicas provocan un contacto directo o indirecto con éstos, ya sea a través del instrumental, equipo odontológico contaminado con saliva, sangre, exudados, etcétera. Por esta razón debe tomarse en cuenta el tipo de contaminación de las piezas de mano por ser parte del equipo de uso cotidiano para realizar tratamientos odontológicos. Objetivos generales:Determinar la carga bacteriana en las piezas de alta velocidad antes y después de su uso en diferentes clínicas de la Facultad de Odontologíade la UV Región Veracruz. Metodología: Investigación transversal, descriptiva y observacional. Material y métodos: Se seleccionaron al azar 30 piezas de mano de los estudiantes de la Universidad Veracruzana Facultad de Odontología Región Veracruz, a las cuales se tomó una muestra con un hisopo de algodón antes y después de su uso en la práctica dental. Se realizaron cultivos con las muestras obtenidas que se observaron durante tres días seguidos bajo microscopio para comprobar la presencia de colonias bacterianas. Resultados: De las30 piezas antes de ser utilizadas se detectó Bacillus grampositivos en24 por ciento de las muestras; en 20 por ciento Bacillus gramnegativos, en 6 por ciento Streptobacillus gram-positivos; en 20 por ciento Staphylococcus grampositivos; en 3 por ciento Cocobacillus gramnegativos y en 22 por ciento Actinomyces gramnegativos. El restante 2 por ciento no reveló unidades formadoras de colonias (UFC). En un segundo muestreo, 33 por ciento desarrolló Bacillus grampositivos, 10 por cientoBacillus gramnegativos, 20 por ciento adquirió Sthapylococcus grampositivos, 3 por ciento Sthapylococcus gramnegativo y 34 por ciento no reveló UFC. Conclusión:En el primer muestreo se detectaron microorganismos en 98% de laspiezas de mano, mientras que en el segundo muestreo 66% se contaminócon microorganismos y en 34% no se observó contaminación.

Introduction: dental activity is exposed to a lot of microorganisms,and clinical interventions have a direct or indirect contact with them.Whether through the instruments, dental equipment contaminatedwith saliva, blood, etc; so you should take into account the type ofcontamination of handpieces for being the most widely used equipmentfor dental treatment. General Objectives: Determine the bacterialload in high-speed parts before and after being used in diff erentclinical uses in Dentistry School at UV, Veracruz. Methodology:Cross-sectional, descriptive and observational research. Materialand methods: 30 pieces of students from the Universidad VeracruzanaSchool of Dentistry, Veracruz region, which a sample was takenwith a swab to pieces before and after use in dental practice wererandomly selected. Cultures with samples obtained observedduring three days in a row microscope to determine the presenceof bacterial colonies were made. Results: Of the 30 pieces beforebeing used 24% of Bacillus Gram-positive samples were found; 20%Bacillus Gram-negative, Gram-positive Streptobacillus 6%; 20%Gram-positive Staphylococcus, 3% developed Coccobacillus Gramnegativeand 22% Gram negative Actinomyces. The remaining 2%no colony forming units development (UFC). In a second sampling;33% developed Bacillus Gram-positive, Gram-negative Bacillus10%, 20% obtained Sthapylococcus Gram-positive, Gram-negativeSthapylococcus 3% and 34% did not develop colony forming unit(CFU). Conclusion: In the first sampling 98% of the pieces were microorganism growth, while in the second 66% and the presence ofmicroorganisms obtained 34% no development.

Evaluation of Three Bacterial Identification Systems for Species Identification of Bacteria Isolated from Bovine Mastitis and Bulk Tank Milk Samples.

A study was conducted to evaluate Sensititre® Automated Reading and Incubation System 2x System (ARIS), API® (API), and Bruker MALDI-TOF MS (MALDI) bacterial species identification systems using 132 diverse bacterial isolates from bovine milk samples and bulk tank milk received at the Penn State Animal Diagnostic Laboratory. The results were compared with 16S rRNA gene sequence analysis, which served as the reference method for species identification. The ARIS, API, and MALDI identified 0%, 40%, and 33.4% of species classified as Gram-positive rod isolates belonging to genera Arthrobacter, Bacillus, Brachybacterium, Brevibacterium, and Corynebacterium, respectively. It was observed that 76.5%, 93.9%, and 96.9% of catalase-negative, Gram-positive cocci (n = 33; Aerococcus, Enterococcus, Lactococcus, Streptococcus) were correctly identified to the species level by ARIS, API, and MALDI, respectively, while 33.4%, 84.5%, and 97.7% of catalase-positive, Gram-positive cocci (n = 45; Kocuria, Staphylococcus) were correctly identified to their species by ARIS, API, and MALDI, respectively. A total of 48 isolates (Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Pantoea, Pasteurella, Providencia, Pseduomonas, Serratia) of Gram-negative bacteria were examined, of which 85.4%, 93.7%, and 95.8% of the isolates were correctly identified to the species level by ARIS, API, and MALDI, respectively. In our laboratory, the MALDI had the least costs associated with consumables and reagents compared to ARIS, API, and 16S rRNA identification methods. Identification of bacterial species was accomplished in <2 h using MALDI and 24 h for ARIS, API, and 16S rRNA identification systems.

Rapid differentiation of cocci/mixed bacteria from rods in voided urine culture of women with uncomplicated urinary tract infections.

OBJECTIVES: To evaluate the ability of laser flow cytometry to predict cocci/mixed growth in the pre-analytical phase of urine specimens. METHODS: We retrospectively reviewed urine samples from women with uncomplicated urinary tract infections from urologic clinics for study. Urine analyses were performed with laser flow cytometry (UF1000i, Sysmex, Kobe, Japan) and then diagrams were generated (forward scatter vs. fluorescent light scatter). Each specimen (bacteria count >357 BACT/µL) was classified as either cocci bacteria or rods/mixed growth according to the diagrams. Standard urine cultures were performed, and the agreement between cultures and the UF1000i interpretations was analyzed with kappa statistics. RESULTS: Finally, 491 specimens met the criteria for analysis. Among the 376 specimens with single bacteria growth, there were 26 gram-positive cocci (13 Streptococci spp., 7 Staphylococci spp., 6 Enterococci spp.), 1 gram-positive rods (Corynebacterium spp.), and 349 gram-negative rods (273 Escherichia coli, 33 Klebsiella spp., 29 Proteus spp., 6 Citrobacter spp., 4 Enterobacter spp., 3 Pseudomonas spp., and 1 Providencia spp.). There were 115 specimens with two bacteria species or more that were regarded as mixed growth. Agreement of rods or cocci/mixed growth between the laser flow cytometry and urine cultures yielded a kappa value of 0.58. The positive and negative predictive rate of the UF1000i for cocci/mixed growth in voided urine culture was 81.8% and 84.7%, respectively. CONCLUSIONS: Through laser flow cytometry, we can predict growth of cocci/mixed growth in the pre-analytical phase of urine culture, thus avoiding unnecessary urine culture and waiting time.

Clinical Significance of Commensal Gram-Positive Rods Routinely Isolated from Patient Samples.

Commensal bacteria from the skin and mucosal surfaces are routinely isolated from patient samples and considered contaminants. The majority of these isolates are catalase-positive Gram-positive rods from multiple genera routinely classified as diphtheroids. These organisms can be seen upon Gram staining of clinical specimens or can be isolated as the predominant or pure species in culture, raising a priori suspicion of a possible involvement in infection. With the development and adoption of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), suspicious isolates are now routinely identified to the species level. In this study, we performed a retrospective data review (2012 to 2015) and utilized site-specific laboratory criteria and chart reviews to identify species within the diphtheroid classification representative of true infection versus contamination. Our data set included 762 isolates from 13 genera constituting 41 bacterial species. Only 18% represented true infection, and 82% were deemed contaminants. Clinically significant isolates were identified in anaerobic wounds (18%), aerobic wounds (30%), blood (5.5%), urine (22%), cerebrospinal fluid (24%), ophthalmologic cultures (8%), and sterile sites (20%). Organisms deemed clinically significant included multiple Actinomyces species in wounds, Propionibacterium species in joints and cerebrospinal fluid associated with central nervous system hardware, Corynebacterium kroppenstedtii (100%) in breast, and Corynebacterium striatum in multiple sites. Novel findings include clinically significant urinary tract infections by Actinomyces neuii (21%) and Corynebacterium aurimucosum (21%). Taken together, these findings indicate that species-level identification of diphtheroids isolated with a priori suspicion of infection is essential to accurately determine whether an isolate belongs to a species associated with specific types of infection.

Clinical significance of coryneform Gram-positive rods from blood identified by MALDI-TOF mass spectrometry and their susceptibility profiles - a retrospective chart review.

With the advent of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), most Gram-positive rods (GPRs) are readily identified; however, their clinical relevance in blood cultures remains unclear. Herein, we assessed the clinical significance of GPRs isolated from blood and identified in the era of MALDI-TOF MS. A retrospective chart review of patients presenting to the Mayo Clinic, Rochester, MN, from January 1, 2013, to October 13, 2015, was performed. Any episode of a positive blood culture for a GPR was included. We assessed the number of bottles positive for a given isolate, time to positivity of blood cultures, patient age, medical history, interpretation of culture results by the healthcare team and whether infectious diseases consultation was obtained. We also evaluated the susceptibility profiles of a larger collection of GPRs tested in the clinical microbiology laboratory of the Mayo Clinic, Rochester, MN from January 1, 2013, to October 31, 2015. There were a total of 246 GPRs isolated from the blood of 181 patients during the study period. 56% (n = 101) were deemed contaminants by the healthcare team and were not treated; 33% (n = 59) were clinically determined to represent true bacteremia and were treated; and 8% (n = 14) were considered of uncertain significance, with patients prescribed treatment regardless. Patient characteristics associated with an isolate being treated on univariate analysis included younger age (P = 0.02), identification to the species level (P = 0.02), higher number of positive blood culture sets (P < 0.0001), lower time to positivity (P < 0.0001), immunosuppression (P = 0.03), and recommendation made by an infectious disease consultant (P = 0.0005). On multivariable analysis, infectious diseases consultation (P = 0.03), higher number of positive blood culture sets (P = 0.0005) and lower time to positivity (P = 0.03) were associated with an isolate being treated. 100, 83, 48 and 34% of GPRs were susceptible to vancomycin, meropenem, penicillin and ceftriaxone, respectively.

Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov.

A novel Gram-stain-negative, rod-shaped, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated 2W32T, was isolated from a marine solar saltern on the coast of Weihai, Shandong Province, China. Strain 2W32T was tolerant to moderate salt conditions. Optimal growth occurred at 33-37 °C (range 20-45 °C) and pH 7.5-8.0 (range pH 7.0-8.5) with 6-10 % (w/v) NaCl (range 2-18 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2W32T shared highest similarity with Aliifodinibius sediminis YIM J21T (94.6 %), Aliifodinibius roseus YIM D15T (94.4 %), Fodinibius salinus YIM C003T (93.6 %), Gracilimonas tropica CL-CB462T (88.6 %) and Balneola vulgaris 13IX/A01/164T (86.4 %) and less than 83.0 % similarity with other species of the phylum Bacteroidetes. The isolate and closely related species formed a novel family-level clade in the phylum Bacteroidetes. The polar lipid profile of the novel isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The dominant cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH) and the sole respiratory quinone was menaquinone 7 (MK-7). The DNA G+C content of strain 2W32T was 47.5 mol %. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain 2W32T represents a novel species within the genus Aliifodinibius, for which the name Aliifodinibius halophilus sp. nov. is proposed. The type strain is 2W32T (=KCTC 42497T=CICC 23869T). In addition, a novel family, Balneolaceae fam. nov., is proposed to accommodate the genera Fodinibius, Aliifodinibius, Gracilimonas and Balneola.

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils.

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively.

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. subtilis (subsp. spizizenii (2) and subsp. inaquosurum (6)), B. amyloliquefaciens (subsp. amyloliquefaciens (4) and subsp. plantarum (4)), B. tequilensis (3), B. pumilus (3) and Bacillus sp. (19). Only six isolates (2.5%) belonged to the genus Aeribacillus represented by A. pallidus (4) and Aeribacillus sp. (2). In this study, B. aerius and B. tequilensis are described for the first time as thermophilic bacteria. Moreover, 71.25%, 50.41% and 5.41% of total strains exhibited high amylolytic, proteolytic or cellulolytic activity respectively.

Quantitative analysis of classical and new putative periodontal pathogens in subgingival biofilm: a case-control study.

BACKGROUND AND OBJECTIVES: A number of species/phylotypes have been newly implicated as putative periopathogens. The objective of this study was to explore associations among classical and new pathogens in subgingival biofilm and to assess their relative importance to chronic periodontitis. MATERIAL AND METHODS: Pooled subgingival biofilm samples were obtained from 40 patients with chronic periodontitis and 40 healthy controls. Taqman q-PCR assays were used to determine the absolute and relative counts of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Parvimonas micra, Filifactor alocis, oral Synergistetes and oral TM7s. Microbial associations were assessed using cluster analysis. Different statistical models were used to explore associations between microbial parameters and periodontitis. RESULTS: The median log and relative counts were lowest for TM7s (4.4 and 0.0016%, respectively) and highest for oral Synergistetes (7.2 and 1.4%, respectively). Oral Synergistetes clustered strongly with the red complex, particularly T. forsythia (100% rescaled similarity). All species/phylotypes except TM7s were significantly associated with periodontitis (Mann-Whitney test; p ≤ 0.005). However, P. gingivalis and F. alocis lost association after adjusting for confounders (ordinal regression). In receiving operator characteristic curve analysis, the log counts of oral Synergistetes were the best markers of periodontitis (82.5% sensitivity and specificity), followed by those of T. forsythia, P. micra and T. denticola. In prediction analysis, however, P. micra was the only microbial predictor of periodontal parameters. CONCLUSIONS: Oral Synergistetes are presented here as new members of the red complex, with relative importance to periodontitis exceeding that of the classical members. P. micra is shown as an important periodontal pathogen warranting more attention.

Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost.

A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0-8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) ( = NBRC 109510(T) = KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

Caldicellulosiruptor changbaiensis sp. nov., a cellulolytic and hydrogen-producing bacterium from a hot spring.

A novel thermophilic bacterial strain, CBS-Z(T), was isolated from a terrestrial hot spring in the Changbai Mountains, PR China. Cells of strain CBS-Z(T) were short straight rods without flagella and had Gram-positive cell walls. Growth was observed at 40-90 °C (optimum 75 °C) and at pH 5.6-8.6 (optimum pH 7.8). The primary end-products from the fermentation of filter paper by strain CBS-Z(T) were acetate, lactate, H2, and CO2. The main cellular fatty acids were iso-C17:0, iso-C14:0 3-OH and C16:0. The G+C content of the genomic DNA was 36.08 mol%. Multiple sequence alignment of the 16S rRNA gene sequence and phylogenetic analyses indicated that strain CBS-Z(T) belongs to the genus Caldicellulosiruptor and the most similar micro-organism was Caldicellulosiruptor saccharolyticus DSM 8903(T) (96.36% 16S rRNA gene sequence similarity); the 16S rRNA gene sequence similarity of strain CBS-Z(T) to other species was below 95%. Based on its phylogenetic and phenotypic characteristics, strain CBS-Z(T) represents a novel species of the genus Caldicellulosiruptor, for which the name Caldicellulosiruptor changbaiensis sp. nov. is proposed. The type strain is CBS-Z(T) ( =DSM 26941(T) =CGMCC 1.5180(T)).

Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester.

An obligately anaerobic bacterium, designated strain GK12(T), was isolated from an anaerobic digester in Fukagawa, Hokkaido Prefecture, Japan. The cells of strain GK12(T) were non-motile, non-spore-forming cocci that commonly occurred in chains. 16S rRNA gene sequence analysis revealed that strain GK12(T) was affiliated with the family Erysipelotrichaceae in the phylum Firmicutes and showed 91.8 % sequence similarity to the most closely related species, Faecalicoccus acidiformans. The strain grew at 30-50 °C (optimally at 40 °C) and at pH 5.5-8.5 (optimally at pH 7.5). The main end product of glucose fermentation was lactate. Yeast extract was required for growth. The strain contained C14 : 0, C14 : 0 1,1-dimethoxyalkane (DMA), C16 : 0 DMA and C18 : 0 DMA as the major cellular fatty acids (>10 % of the total). The polar lipid profile was composed of phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The whole-cell sugars were galactose, rhamnose and ribose. The cell-wall murein contained alanine, glutamic acid, lysine, serine and threonine, but not diaminopimelic acid. The G+C content of the genomic DNA was 47.7 mol%. Based on phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species, Catenisphaera adipataccumulans gen. nov., sp. nov., is proposed to accommodate strain GK12(T) ( = NBRC 108915(T) = DSM 25799(T)).

Bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Nocardia, Rhodococcus, Kocuria, Gordonia, Tsukamurella, and Listeria species.

We evaluated whether the Bruker Biotyper matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system provides accurate species-level identifications of 147 isolates of aerobically growing Gram-positive rods (GPRs). The bacterial isolates included Nocardia (n = 74), Listeria (n = 39), Kocuria (n = 15), Rhodococcus (n = 10), Gordonia (n = 7), and Tsukamurella (n = 2) species, which had all been identified by conventional methods, molecular methods, or both. In total, 89.7% of Listeria monocytogenes, 80% of Rhodococcus species, 26.7% of Kocuria species, and 14.9% of Nocardia species (n = 11, all N. nova and N. otitidiscaviarum) were correctly identified to the species level (score values, ≥ 2.0). A clustering analysis of spectra generated by the Bruker Biotyper identified six clusters of Nocardia species, i.e., cluster 1 (N. cyriacigeorgica), cluster 2 (N. brasiliensis), cluster 3 (N. farcinica), cluster 4 (N. puris), cluster 5 (N. asiatica), and cluster 6 (N. beijingensis), based on the six peaks generated by ClinProTools with the genetic algorithm, i.e., m/z 2,774.477 (cluster 1), m/z 5,389.792 (cluster 2), m/z 6,505.720 (cluster 3), m/z 5,428.795 (cluster 4), m/z 6,525.326 (cluster 5), and m/z 16,085.216 (cluster 6). Two clusters of L. monocytogenes spectra were also found according to the five peaks, i.e., m/z 5,594.85, m/z 6,184.39, and m/z 11,187.31, for cluster 1 (serotype 1/2a) and m/z 5,601.21 and m/z 11,199.33 for cluster 2 (serotypes 1/2b and 4b). The Bruker Biotyper system was unable to accurately identify Nocardia (except for N. nova and N. otitidiscaviarum), Tsukamurella, or Gordonia species. Continuous expansion of the MALDI-TOF MS databases to include more GPRs is necessary.

Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory.

Reported matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification rates of Gram-positive rods (GPR) are low compared to identification rates of Gram-positive cocci. In this study, three sample preparation methods were compared for MALDI-TOF MS identification of 190 well-characterized GPR strains: direct transfer, direct transfer-formic acid preparation, and ethanol-formic acid extraction. Using the interpretation criteria recommended by the manufacturer, identification rates were significantly higher for direct transfer-formic acid preparation and ethanol-formic acid extraction than for direct transfer. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification rates. In a subsequent prospective study, 215 clinical GPR isolates were analyzed by MALDI-TOF MS, and the results were compared to those for identification using conventional methods, with discrepancies being resolved by 16S rRNA and rpoB gene analysis. Using the direct transfer-formic acid preparation and a species cutoff of 1.7, congruencies on the genus and species levels of 87.4% and 79.1%, respectively, were achieved. In addition, the rate of nonidentified isolates dropped from 12.1% to 5.6% when using an extended database, i.e., the Bruker database amended by reference spectra of the 190 GPR of the retrospective study. Our data demonstrate three ways to improve GPR identification by the Bruker MALDI Biotyper, (i) optimize sample preparation using formic acid, (ii) reduce cutoff scores for species identification, and (iii) expand the database. Based on our results, we suggest an identification algorithm for the clinical laboratory combining MALDI-TOF MS with nucleic acid sequencing.