Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria

Methane oxidation coupled to vanadate reduction in a membrane biofilm batch reactor under hypoxic condition

This study shows vanadate (V(V)) reduction in a methane (CH₄) based membrane biofilm batch reactor when the concentration of dissolved oxygen (O₂) was extremely low. V(IV) was the dominant products formed from V(V) bio-reduction, and majority of produced V(IV) transformed into precipitates with green color. Quantitative polymerase chain reaction and Illumina sequencing analysis showed that archaea methanosarcina were significantly enriched. Metagenomic predictive analysis further showed the enrichment of genes associated with reverse methanogenesis pathway, the key CH₄-activating mechanism for anaerobic methane oxidation (AnMO), as well as the enrichment of genes related to acetate synthesis, in archaea. The enrichment of aerobic methanotrophs Methylococcus and Methylomonas implied their role in CH₄ activation using trace level of O₂, or their participation in V(V) reduction.

Effects of Chestnut Tannin Extract, Vescalagin and Gallic Acid on the Dimethyl Acetals Profile and Microbial Community Composition in Rumen Liquor: An In Vitro Study

The addition of polyphenol extracts in ruminant diets is an effective strategy to modulate rumen microflora. The aim of this in vitro trial was to study the effects of chestnut tannin extract (CHT), vescalagin (VES) and gallic acid (GAL) on dietary fibre degradability and on the dimethyl acetals (DMA) profile and microbial community composition of rumen liquor. Four diets (basal diet; basal diet plus CHT; basal diet plus VES; basal diet plus GAL) were fermented for 24 h using ewe rumen liquor. At the end of the fermentation, the microbial communities were characterized by sequencing the 16S rRNA gene. The DMA profile was analyzed by gas chromatography. Chestnut tannin extract did not affect fibre degradability, whereas VES and GAL showed a detrimental effect. The presence of CHT, VES and GAL influenced the concentration of several DMA (i.e., 12:0, 13:0, 14:0, 15:0, 18:0 and 18:1 trans-11), whereas the composition of the microbial community was marginally affected. The inclusion of CHT led to the enrichment of the genera Anaerovibrio, Bibersteinia, Escherichia/Shigella, Pseudobutyrivibrio and Streptococcus. The results of this study support the hypothesis that the activity of CHT is due to the synergistic effect of all components rather than the property of a single component.

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing

We set out to identify the viable and total bacterial content in milk as it passes through a large-scale, dairy product manufacturing plant for pasteurization, concentration, separation, blending, and storage prior to cheese manufacture. A total of 142 milk samples were collected from up to 10 pieces of equipment for a period spanning 21 h on two collection dates in the spring and late summer of 2014. Bacterial composition in the milk was determined by 16S rRNA marker gene, high-throughput DNA sequencing. Milk samples from the late summer were paired such that half were treated with propidium monoazide (PMA) to enrich for viable cells prior to quantification by PCR and identification by DNA sequence analysis. Streptococcus had the highest median relative abundance across all sampling sites within the facility on both sampling dates. The proportions of Anoxybacillus, Thermus, Lactococcus, Lactobacillus, Micrococcaceae, and Pseudomonas were also elevated in some samples. Viable cells detected by PMA treatment showed that Turicibacter was enriched after high-temperature short-time pasteurization, whereas proportions of Staphylococcus were significantly reduced. Using clean-in-place (CIP) times as a reference point, Bacillus, Pseudomonas, and Anoxybacillus were found in high relative proportions in several recently cleaned silos (<19 h since CIP). At later times (>19 h after CIP), 10 of 11 silos containing elevated viable cell numbers were enriched in Acinetobacter and/or Lactococcus These results show the tremendous point-to-point and sample-dependent variations in bacterial composition in milk during processing.IMPORTANCE Milk undergoes sustained contact with the built environment during processing into finished dairy products. This contact has the potential to influence the introduction, viability, and growth of microorganisms within the milk. Currently, the population dynamics of bacteria in milk undergoing processing are not well understood. Therefore, we measured for total and viable bacterial composition and cell numbers in milk over time and at different processing points in a cheese manufacturing facility in California. Our results provide new perspectives on the dramatic variations in microbial populations in milk during processing even over short amounts of time. Although some of the changes in the milk microbiota were predictable (e.g., reduced viable cell numbers after pasteurization), other findings could not be easily foreseen based on knowledge of bacteria contained in raw milk or when the equipment was last cleaned. This information is important for predicting and controlling microbial spoilage contaminants in dairy products.

Relationship of oral conditions to the incidence of infective endocarditis in periodontitis patients with valvular heart disease: a cross-sectional study

OBJECTIVES

Infective endocarditis (IE) is a life-threatening infectious disease, but the pathogenesis of the disease remains uncertain. The objective of this study was to examine whether oral infectious conditions are associated with the occurrence of IE in valvular heart disease (VHD) patients.

MATERIALS AND METHODS

A total of 119 periodontitis (P) patients with or without VHD were enrolled, and cross-sectional analyses were performed. Patients were classified as follows: (1) mild-to-moderate P without VHD, (2) mild-to-moderate P with VHD, (3) severe P without VHD, or (4) severe P with VHD. A total of 78 VHD patients were classified as (1) VHD without IE or (2) VHD with IE. Conditional logistic regression analysis was performed to compute the odds ratio (OR) and 95% confidence interval (CI).

RESULTS

No significant differences were observed between patients with or without VHD in oral conditions. A significant increase in the percentage of alveolar bone loss in VHD patients with IE was observed compared with that of patients without IE. The ratio of both Porphyromonas gingivalis (Pg) IgG titer > 1.68 and Pg fimA type II genotype in patients with IE was significantly higher than in patients without IE. There was a significant correlation between the occurrence of IE and clinical oral findings (number of remaining teeth: OR, 0.17; rate of alveolar bone loss > 40%: OR, 11.8).

CONCLUSIONS

VHD patients with IE might have severe periodontitis compared with patients without IE, although further investigation will be needed because this is based on only 7 VHD patients with IE.

CLINICAL RELEVANCE

The patients with IE had fewer remaining teeth, more advanced bone resorption compared with those of patients without IE. These findings suggest a possible association between the occurrence of IE and periodontal infection.

BD-2 and BD-3 increase skin flap survival in a model of ischemia and Pseudomonas aeruginosa infection

The main aim of this work was to study the usefulness of human β-defensins 2 (BD-2) and 3 (BD-3), which are part of the innate immune system, in the treatment of infected ischemic skin flaps. We investigated the effect of transducing rat ischemic skin flaps with lentiviral vectors encoding human BD-2, BD-3, or both BD-2 and BD-3, to increase flap survival in the context of a P. aeruginosa infection associated with a foreign body. The secondary endpoints assessed were: bacterial counts, and biofilm formation on the surface of the foreign body. A local ischemic environment was created by producing arterialized venous flaps in the left epigastric region of rats. Flaps were intentionally infected by placing underneath them two catheters with 105 CFU of P. aeruginosa before the surgical wounds were hermetically closed. Flap biopsies were performed 3 and 7 days post-operatively, and the specimens submitted to immunohistochemical analysis for BD-2 and BD-3, as well as to bacterial quantification. Subsequently, the catheter segments were analyzed with scanning electron microscopy (SEM). Flaps transduced with BD-2 and BD-3 showed expression of these defensins and presented increased flap survival. Rats transduced with BD-3 presented a net reduction in the number of P. aeruginosa on the surface of the foreign body and lesser biofilm formation.

Butyrate production in patients with end-stage renal disease

Background: Chronic kidney disease (CKD) is associated with a decreased intestinal barrier function, causing bacterial translocation over the intestinal wall and triggering a systemic inflammatory response. Butyrate, a short-chain fatty acid produced by certain bacterial strains, is considered instrumental to keep the intestinal barrier intact. There are indications that a decreased amount of these specific bacterial species is part of the cause of the decreased intestinal barrier function in CKD. The aim of this study is (i) to determine if Dutch patients with end-stage renal disease (ESRD) have a decreased amount of butyrate-producing species and butyrate-producing capacity and (ii) whether this correlates with systemic inflammation. Methods: We used qPCR to evaluate the most abundant butyrate-producing species F. prauznitzii, E. rectale and Roseburia spp. and the BCoAT gene, which reflects the butyrogenic capacity of the intestinal microbiota. Fecal samples were collected from healthy kidney donors (n=15), preemptive renal transplant recipients (n=4) and dialysis patients (n=31). Markers of inflammation (CRP and IL-6) and intestinal permeability (D-lactate) were measured in plasma. Results: Patients with ESRD did not have a significantly decreased amount F. prauznitzii, E. rectale and Roseburia spp. or the BCoAT gene. Neither was there a significant correlation with CRP, IL-6 or D-lactate. On the individual level, there were some patients with decreased BCoAT levels and increased levels of CRP, IL-6 and D-lactate. Conclusions: Patients with ESRD do not have a decreased amount of the most abundant butyrate-producing species nor a decreased butyrate-producing capacity.

Intestinal iNKT cells migrate to liver and contribute to hepatocyte apoptosis during alcoholic liver disease

We investigated the migration of intestinal immune cells to the liver and their contribution to alcoholic liver disease. In mice fed ethanol, we found that an increased number of invariant natural killer T (iNKT) cells, which respond to the antigen presented by CD1d, migrated from mesenteric lymph nodes to the liver. iNKT cells react to lipid antigens, so we studied their activities in mice with intestinal epithelial cell-specific deletion of Pparg (PpargΔIEC) as a model for altering intestinal lipidomic profiles. Levels of CD1d increased in intestines of ethanol-fed PpargΔIEC mice, and in cell-tracking experiments, more iNKT cells migrated to the liver, compared with mice without disruption of Pparg. Livers of PpargΔIEC mice had increased markers of apoptosis and liver injury after ethanol feeding. iNKT cells isolated from livers of ethanol-fed PpargΔIEC mice induced apoptosis of cultured hepatocytes. An inhibitor of iNKT cells reduced ethanol-induced liver injury in PpargΔIEC mice. Duodenal tissues from patients with alcohol-use disorder have been found to have increased levels of CD1d compared with tissues from patients without alcohol overuse. Ethanol use, therefore, activates iNKT cells in the intestine to migrate to liver, where they-along with the resident hepatic iNKT cells-contribute to hepatocyte death and injury. NEW & NOTEWORTHY In this article, we studied migration of intestinal immune cells into the liver in response to ethanol-induced liver disease. We found that chronic ethanol feeding induces expression of CD1d by enterocytes, which activate invariant natural killer T (iNKT) cells in mesenteric lymph nodes; activation is further increased with loss of peroxisome proliferator-activated receptor gamma gene and altered lipid profiles. The activated iNKT cells migrate into the liver, where they promote hepatocyte apoptosis. Patients with alcohol use disorder have increased expression of CD1d in the small intestine. Strategies to block these processes might be developed to treat alcoholic liver disease.

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

Bacterial species and total bacterial load in the distal oesophagus in patients with and without clinical gastric reflux

AIMS

The purpose of this study is to compare distal oesophagus of persons with and without gastric reflux in terms of bacterial load and presence of certain bacterial species.

METHODS AND RESULTS

Two biopsy specimens were obtained from the distal oesophagus at 5 cm above the gastroesophageal junction of each of the 50 patients (20 with normal oesophagus and 30 with reflux oesophagitis) under endoscopic examination and used for histological examination and DNA isolation. We used a real-time PCR-based assay to quantify the bacterial load and the presence of certain bacterial species from one of the biopsy samples. The biopsy specimens taken from the patients with reflux oesophagitis were consistent with gastroesophageal reflux disease (GERD). The bacterial load did not significantly differ between the groups (P < 0·005).

CONCLUSION

While there was no difference between the bacterial load in the two groups, variation was observed in bacterial species. Most of the bacteria identified in distal oesophagus of the patients with gastroesophageal reflux were Gram negative.

SIGNIFICANCE AND IMPACT OF THE STUDY

The human oesophagus was considered sterile until quite recently. Molecular techniques displayed the presence of a diverse bacterial species in the oesophagus. Although it is known that dysbiosis in the oesophagus causes GERD, and that Barrett's oesophagus can trigger the development of oesophageal adenocarcinoma, its etiopathogenesis is not clear. A limited number of published studies support the importance of the present study.

Genetic effects on the commensal microbiota in inflammatory bowel disease patients

Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease (IBD), and dozens of IBD genetic variants have been identified in genome-wide association studies. However, the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility remains unclear. Here, we studied the association between four major genetic variants associated with an increased risk of IBD and bacterial taxa in up to 633 IBD cases. We performed systematic screening for associations, identifying and replicating associations between NOD2 variants and two taxa: the Roseburia genus and the Faecalibacterium prausnitzii species. By exploring the overall association patterns between genes and bacteria, we found that IBD risk alleles were significantly enriched for associations concordant with bacteria-IBD associations. To understand the significance of this pattern in terms of the study design and known effects from the literature, we used counterfactual principles to assess the fitness of a few parsimonious gene-bacteria-IBD causal models. Our analyses showed evidence that the disease risk of these genetic variants were likely to be partially mediated by the microbiome. We confirmed these results in extensive simulation studies and sensitivity analyses using the association between NOD2 and F. prausnitzii as a case study.

Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome

We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn's colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR < 0.05) in microbiota were observed between macroscopically disease unaffected and affected regions of resected ileum in ileal CD patients. Accordingly, analysis of the effects of genetic and clinical factors were restricted to disease unaffected regions of the ileum. Beta-diversity differed across the three disease categories by PERMANOVA (p < 0.001), whereas no significant differences in alpha diversity were noted. Using negative binomial models, we confirmed significant effects of IBD phenotype, C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6-12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.

Resolvin D2 Induces Resolution of Periapical Inflammation and Promotes Healing of Periapical Lesions in Rat Periapical Periodontitis

Periapical periodontitis results from pulpal infection leading to pulpal necrosis and resorption of periapical bone. The current treatment is root canal therapy, which attempts to eliminate infection and necrotic tissue. But, in some cases periapical inflammation doesn't resolve even after treatment. Resolvins belongs to a large family of specialized pro-resolving lipid mediators that actively resolves inflammation signaling via specific receptors. Resolvin D2 (RvD2), a metabolite of docosahexaenoic acid (DHA), was tested as an intracanal medicament in rats in vivo. Mechanism was evaluated in rat primary dental pulp cells (DPCs) in vitro. The results demonstrate that RvD2 reduces inflammatory cell infiltrate, periapical lesion size, and fosters pulp like tissue regeneration and healing of periapical lesion. RvD2 enhanced expression of its receptor, GPR18, dentin matrix acidic phosphoprotein 1 (DMP1) and mineralization in vivo and in vitro. Moreover, RvD2 induces phosphorylation of Stat3 transcription factor in dental pulp cells. We conclude that intracanal treatment with RvD2 resolves inflammation and promoting calcification around root apex and healing of periapical bone lesions. The data suggest that RvD2 induces active resolution of inflammation with pulp-like tissue regeneration after root canal infection and thus maybe suitable for treating periapical lesions.

Coleus amboinicus (Lour.) leaves as a modulator of ruminal methanogenesis and biohydrogenation in vitro

Active plant metabolites (APM) are recognized as modifiers of ruminal microbial fermentation including methanogenesis and biohydrogenation of fatty acids (FA). Coleus amboinicus Lour. leaves (CAL) are rich in several APM, which could serve as ruminal fermentation modulators. A phytochemical analysis showed that CAL contain phenolic acids (10.4 mg·g-1 dry matter [DM]; high in rosmarinic acid), flavonoids (2.6 mg·g-1 DM), diterpenes (2 mg·g-1 DM), and linolenic acid (35.4 g (100 g)-1 FA). This study aimed to investigate the effect of CAL on ruminal methanogenesis and biohydrogenation as well as basic fermentation characteristics and microbial populations. The in vitro experiment was carried out using Hohenheim gas test system with 40 mL of buffered ruminal fluid incubated for 24 h at 39 °C in anaerobic conditions. Approximately 400 mg (DM basis) of total mixed ration (TMR) was used as a control substrate and the CAL substrate was used at doses of 10, 20, 40, and 80 mg DM replacing equal amounts of TMR. Addition of CAL decreased methane production up to 30% linearly as the amount of CAL increased (P < 0.05). In vitro dry matter digestibility and ammonia tended to increase with increasing doses of CAL. Concentration of total volatile fatty acids was not affected by the CAL although there appeared to be a minor positive linear trend; however, acetate, butyrate, and isobutyrate proportion increased quadratically (P < 0.001). CAL tended to linearly increase α-linolenic acid and conjugated linoleic acid as well as increased stearic acid concentration in buffered ruminal fluid. CAL particularly increased total protozoa and bacterial populations during fermentation, but inhibited methanogens. It is concluded that the CAL may be promising to be used as a feed additive to decrease methanogenesis as well as biohydrogenation of FA in the rumen.

Accelerated inflammation in peripheral artery disease patients with periodontitis

Purpose

Peripheral artery disease (PAD) is a form of arteriosclerosis that occurs in the extremities and involves ischemia. Previous studies have reported that patients with periodontitis are at high risk for PAD. However, the relationship between these 2 diseases has not yet been fully elucidated. In this cross-sectional study, we investigated this relationship by comparing patients with PAD to those with arrhythmia (ARR) as a control group.

Methods

A large-scale survey was conducted of patients with cardiovascular disease who visited Tokyo Medical and Dental University Hospital. We investigated their oral condition and dental clinical measurements, including probing pocket depth, bleeding on probing, clinical attachment level, and number of missing teeth; we also collected salivary and subgingival plaque samples and peripheral blood samples. All patients with PAD were extracted from the whole population (n=25), and a matching number of patients with ARR were extracted (n=25). Simultaneously, ARR patients were matched to PAD patients in terms of age, gender, prevalence of diabetes, hypertension, dyslipidemia, obesity, and the smoking rate (n=25 in both groups). Real-time polymerase chain reaction was performed to measure the bacterial counts, while the enzyme-linked immunosorbent assay method was used to measure anti-bacterial antibody titers and proinflammatory cytokine levels in serum.

Results

PAD patients had more missing teeth (18.4±2.0) and higher serum levels of C-reactive protein (1.57±0.85 mg/dL) and tumor necrosis factor-alpha (70.3±5.7 pg/mL) than ARR patients (12.0±1.7, 0.38±0.21 mg/dL, and 39.3±4.5 pg/mL, respectively). Meanwhile, no statistically significant differences were found in other dental clinical measurements, bacterial antibody titers, or bacterial counts between the 2 groups.

Conclusions

Our findings suggested that PAD patients had poorer oral and periodontal state with enhanced systemic inflammation.

Effects of chitosan and whole raw soybeans on ruminal fermentation and bacterial populations, and milk fatty acid profile in dairy cows

The objective of this study was to evaluate whether providing chitosan (CHI) to cows fed diets supplemented with whole raw soybeans (WRS) would affect the nutrient intake and digestibility, ruminal fermentation and bacterial populations, microbial protein synthesis, N utilization, blood metabolites, and milk yield and composition of dairy cows. Twenty-four multiparous Holstein cows (141 ± 37.1 d in milk, 38.8 ± 6.42 kg/d of milk yield; mean ± SD) were enrolled to a 4 × 4 Latin square design experiment with 23-d periods. Cows were blocked within Latin squares according to milk yield, days in milk, body weight, and rumen cannula (n = 8). A 2 × 2 factorial treatment arrangement was randomly assigned to cows within blocks. Treatments were composed of diets with 2 inclusion rates of WRS (0 or 14% diet dry matter) and 2 doses of CHI (0 or 4 g/kg of dry matter, Polymar Ciência e Nutrição, Fortaleza, Brazil). In general, CHI+WRS negatively affected nutrient intake and digestibility of cows, decreasing milk yield and solids production. The CHI increased ruminal pH and decreased acetate to propionate ratio, and WRS reduced NH3-N concentration and acetate to propionate in the rumen. The CHI reduced the relative bacterial population of Butyrivibrio group, whereas WRS decreased the relative bacterial population of Butyrivibrio group, and Fibrobacter succinogenes, and increased the relative bacterial population of Streptococcus bovis. No interaction effects between CHI and WRS were observed on ruminal fermentation and bacterial populations. The CHI+WRS decreased N intake, microbial N synthesis, and N secreted in milk of cows. The WRS increased N excreted in feces and consequently decreased the N excreted in urine. The CHI had no effects on blood metabolites, but WRS decreased blood concentrations of glucose and increased blood cholesterol concentration. The CHI and WRS improved efficiency of milk yield of cows in terms of fat-corrected milk, energy-corrected milk, and net energy of lactation. The CHI increased milk concentration [g/100 g of fatty acids (FA)] of 18:1 trans-11, 18:2 cis-9,cis-12, 18:3 cis-9,cis-12,cis-15, 18:1 cis-9,trans-11, total monounsaturated FA, and total polyunsaturated FA. The WRS increased total monounsaturated FA, polyunsaturated FA, and 18:0 to unsaturated FA ratio in milk of cows. Evidence indicates that supplementing diets with unsaturated fat sources along with CHI negatively affects nutrient intake and digestibility of cows, resulting in less milk production. Diet supplementation with CHI or WRS can improve feed efficiency and increases unsaturated FA concentration in milk of dairy cows.

Grading system for periodontitis by analyzing levels of periodontal pathogens in saliva

Periodontitis is an infectious disease that is associated with microorganisms that colonize the tooth surface. Clinically, periodontal condition stability reflects dynamic equilibrium between bacterial challenge and host response. Therefore, periodontal pathogen assessment can assist in the early detection of periodontitis. Here we developed a grading system called the periodontal pathogen index (PPI) by analyzing the copy numbers of multiple pathogens both in healthy and chronic periodontitis patients. We collected 170 mouthwash samples (64 periodontally healthy controls and 106 chronic periodontitis patients) and analyzed the salivary 16S rRNA levels of nine pathogens using multiplex, quantitative real-time polymerase chain reaction. Except for Aggregatibacter actinomycetemcomitans, copy numbers of all pathogens were significantly higher in chronic periodontitis patients. We classified the samples based on optimal cut-off values with maximum sensitivity and specificity from receiver operating characteristic curve analyses (AUC = 0.91, 95% CI: 0.87-0.96) into four categories of PPI: Healthy (1-40), Moderate (41-60), At Risk (61-80), and Severe (81-100). PPI scores were significantly higher in all chronic periodontitis patients than in the controls (odds ratio: 31.7, 95% CI: 13.41-61.61) and were associated with age, scaling as well as clinical characteristics including clinical attachment level and plaque index. Our PPI grading system can be clinically useful for the early assessment of pathogenic bacterial burden and follow-up monitoring after periodontitis treatment.

Selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans by antisense peptide nucleic acids

Peptide nucleic acids (PNA) are DNA/RNA analogs in which the sugar-phosphate backbone is replaced by N-2-aminoethylglycine. PNA are widely used for experimental antisense therapy due to their strong affinity to mRNA. By targeting specific genes, protein synthesis and the growth of bacteria or cancer cells can be inhibited by PNA. Here, we report the design and evaluation of antisense PNA for selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, potent pathogens associated with periodontitis. Antisense PNA against groEL and acpP were prepared with carrier peptide (KFFKFFKFFK). Anti-groEL PNA for P. gingivalis specifically inhibited growth in a dose-dependent manner, and growth was inhibited for 5 h at a concentration of 3 μM. Anti-groEL PNA for A. actinomycetemcomitans inhibited growth for 2 h at a concentration of 3 μM with reduced GroEL protein expression. Anti-acpP PNA did not show a marked growth inhibitory effect on either species. Although further studies are needed to develop more effective antisense PNA for both species, anti-groEL PNA may be potentially useful species-specific antibacterial tools against oral pathogens.

Association between periodontitis and spontaneous abortion: A case-control study

BACKGROUND

Spontaneous abortion, or miscarriage, is a complication of pregnancy which can severely affect women both physically and psychologically. We investigated the associations of periodontitis and periodontopathic bacteria with spontaneous abortion.

METHODS

We conducted a matched case-control study in two tertiary hospitals in Khon Kaen, Thailand. Cases were 85 women with spontaneous abortion at <20 weeks of gestation matched to 85 controls on age, gestational age, and hospital. Full-mouth periodontal examinations were performed. Periodontitis was defined as at least one site with probing depth ≥5 mm and clinical attachment level ≥2 mm at the same site. Subgingival plaque samples were collected to determine the levels of Porphyromonas gingivalis, Tannerella forsythia, and Fusobacterium nucleatum using real time polymerase chain reaction.

RESULTS

The cases were significantly more likely to have periodontitis (50.6%) than the controls (21.2%; P = 0.007). Conditional logistic regression revealed a crude odds ratio (OR) of 4.1 for the association between periodontitis and spontaneous abortion (95% confidence interval [CI] = 1.9-8.9, P = 0.001). The OR decreased, but was still significant, after controlling for previous miscarriage (OR = 3.3, 95% CI = 1.4-7.8, P = 0.006). There was no significant association between the levels of periodontopathic bacteria and spontaneous abortion. Increased levels of P. gingivalis and F. nucleatum were associated with periodontitis in both case and control groups. Association between increased T. forsythia levels and periodontitis was observed only in the case women.

CONCLUSIONS

Periodontitis was more common in women with spontaneous abortions as compared with matched controls. Levels of periodontopathic bacteria was not associated with spontaneous abortion in this population.

Orthogonal test design for optimization of the extraction of essential oil from Asarum heterotropoides var. Mandshuricum and evaluation of its antibacterial activity against periodontal pathogens

The optimum extraction conditions of essential oil from Asarum heterotropoides var. Mandshuricum applied by an orthogonal L₉(3³) test were a water-to-raw material ratio of 17, a particle size of D ₉₅ ≤ 3.8 mm and an extraction time of 2 h. In ingredient analysis, gas chromatography/mass spectrometry analysis identified the main components of essential oil as methyl eugenol (45.95%), safrole (17.48%) and 3,5-dimethoxytoluene (10.30%) orderly. In vitro, the minimum inhibitory concentration and minimum bactericidal concentration of essential oil were 0.01 and 0.02% against F. nucleatum, 0.04 and 0.08% against P. intermedia, and 0.005 and 0.005% against P. gingivalis. In vivo, administration of essential oil significantly suppressed alveolar bone resorption induced by F. nucleatum, with bone levels remaining comparable to non-infected mice. These results of antibacterial activity of essential oil in vitro and in vivo show the inhibition of periodontal pathogens and therapy of alveolar bone resorption in mice, suggesting that its essential oil could be a potential natural therapeutic agent for treatment of periodontitis in human beings.

Daylight exposure modulates bacterial communities associated with household dust

BACKGROUND

Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model "rooms" with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities.

RESULTS

Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community.

CONCLUSIONS

Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings.

Relationship between Candida albicans and Streptococcus mutans in early childhood caries, evaluated by quantitative PCR

Background: The aim of this study was to analyze the synergistic relationship between Candida albicans and Streptococcus mutans in children with early childhood caries (ECC) experience.

Methods: Dental plaque and unstimulated saliva samples were taken from 30 subjects aged 3-5 years old, half with (n=15, dmft > 4) and half without (n=15) ECC. The abundance of C. albicans and S. mutans and relative to total bacteria load were quantify by real-time PCR (qPCR). This method was also employed to investigate the mRNA expression of glycosyltransferase ( gtfB) gene in dental plaque. Student’s t-test and Pearson’s correlation were used to perform statistical analysis.

Results: Within the ECC group, the quantity of both microorganisms were higher in the saliva than in dental plaque. The ratio of C. albicans to total bacteria was higher in saliva than in plaque samples (p < 0.05). We observed the opposite for S. mutans (p < 0.05). The different value of C. albicans and S. mutans in saliva was positively correlated, and negatively correlated in dental plaque. Transcription level of S. mutans gtfB showed a positive correlation with C. albicans concentration in dental plaque. 

Conclusion:C. albicans has a positive correlation with cariogenic traits of S. mutans in ECC-related biofilm of young children.

Residual feed intake in beef cattle and its association with carcass traits, ruminal solid-fraction bacteria, and epithelium gene expression

Background

Residual feed intake (RFI) describes an animal’s feed efficiency independent of growth performance. The objective of this study was to determine differences in growth performance, carcass traits, major bacteria attached to ruminal solids-fraction, and ruminal epithelium gene expression between the most-efficient and the least-efficient beef cattle. One-hundred and forty-nine Red Angus cattle were allocated to three contemporary groups according to sex and herd origin. Animals were fed a finishing diet in confinement for 70 d to determine the RFI category for each. Within each group, the two most-efficient (n = 6; RFI coefficient = − 2.69 ± 0.58 kg dry matter intake (DMI)/d) and the two least-efficient animals (n = 6; RFI coefficient = 3.08 ± 0.55 kg DMI/d) were selected. Immediately after slaughter, ruminal solids-fraction and ruminal epithelium were collected for bacteria relative abundance and epithelial gene expression analyses, respectively, using real-time PCR.

Results

The most-efficient animals consumed less feed (P = 0.01; 5.03 kg less DMI/d) compared with the least-efficient animals. No differences (P > 0.10) in initial body weight (BW), final BW, and average daily gain (ADG) were observed between the two RFI classes. There were no significant RFI × sex effects (P > 0.10) on growth performance. Compared with the least-efficient group, hot carcass weight (HCW), ribeye area (REA), and kidney, pelvic, and heart fat (KPH) were greater (P ≤ 0.05) in the most-efficient cattle. No RFI × sex effect (P > 0.10) for carcass traits was detected between RFI groups. Of the 10 bacterial species evaluated, the most-efficient compared with least efficient cattle had greater (P ≤ 0.05) relative abundance of Eubacterium ruminantium, Fibrobacter succinogenes, and Megasphaera elsdenii, and lower (P ≤ 0.05) Succinimonas amylolytica and total bacterial density. No RFI × sex effect on ruminal bacteria was detected between RFI groups. Of the 34 genes evaluated in ruminal epithelium, the most-efficient cattle had greater (P ≤ 0.05) abundance of genes involved in VFA absorption, metabolism, ketogenesis, and immune/inflammation-response. The RFI × sex interactions indicated that responses in gene expression between RFI groups were due to differences in sex. Steers in the most-efficient compared with least-efficient group had greater (P ≤ 0.05) expression of SLC9A1, HIF1A, and ACO2. The most-efficient compared with least-efficient heifers had greater (P ≤ 0.05) mRNA expression of BDH1 and lower expression (P ≤ 0.05) of SLC9A2 and PDHA1.

Conclusions

The present study revealed that greater feed efficiency in beef cattle is associated with differences in bacterial species and transcriptional adaptations in the ruminal epithelium that might enhance nutrient delivery and utilization by tissues. The lack of RFI × sex interaction for growth performance and carcass traits indicates that sex may not play a major role in improving these phenotypes in superior RFI beef cattle. However, it is important to note that this result should not be considered a solid biomarker of efficient beef cattle prior to further examination due to the limited number of heifers compared with steers used in the study.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0283-8) contains supplementary material, which is available to authorized users.

Role of systemic infection, cross contaminations and super-shedders in Salmonella carrier state in chicken

Carriage of Salmonella is often associated with a high level of bacterial excretion and generally occurs after a short systemic infection. However, we do not know whether this systemic infection is required or whether the carrier-state corresponds to continuous reinfection or real persistence in caecal tissue. The use of a Salmonella Enteritidis bamB mutant demonstrated that a carrier-state could be obtained in chicken in the absence of systemic infection. The development of a new infection model in isolator showed that a marked decrease in animal reinfection and host-to-host transmission between chicks led to a heterogeneity of S. Enteritidis excretion and colonization contrary to what was observed in cages. This heterogeneity of infection was characterized by the presence of super-shedders, which constantly disseminated Salmonella to the low-shedder chicks, mainly through airborne movements of contaminated dust particles. The presence of super-shedders, in the absence of host-to-host transmission, demonstrated that constant reinfection was not required to induce a carrier-state. Finally, our results suggest that low-shedder chicks do not have a higher capability to destroy Salmonella but instead can block initial Salmonella colonization. This new paradigm opens new avenues to improve understanding of the carrier-state mechanisms and to define new strategies to control Salmonella infections.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ileum terminal antibiotic infusion affects jejunal and colonic specific microbial population and immune status in growing pigs

Background

Compared with oral antibiotics (primarily disrupt foregut microbiota), the present study used antibiotics with ileum terminal infusion to disrupt the hindgut microbiota, and investigated the changes in specific bacterial composition and immune indexes in the jejunum and colon, and serum of growing pigs. Twelve barrows (45 d of age, 12.08 ± 0.28 kg) fitted with a T-cannula at the terminal ileum, were randomly assigned to two groups and infused either saline without antibiotics (Control) or with antibiotics (Antibiotic) at the terminal ileum. After 25 d experiment, all pigs were euthanized for analyzing bacterial composition and immune status.

Results

Ileum terminal antibiotic infusion (ITAI) altered dominant bacteria counts, with a decrease in Bifidobacterium, Clostridium cluster IV and Clostridium cluster IV in the colon (P < 0.05), and an increase in Escherichia coli in the jejunum (P < 0.05). ITAI decreased (P < 0.05) short-chain fatty acids concentrations in the colon. ITAI decreased interleukin-8 (IL-8), IL-10 and secretory immunoglobulin A (sIgA) concentrations, and down-regulated IL-10, Mucin-1 (MUC1), Mucin-2 (MUC2) and zonula occludens-1 (ZO-1) mRNA expression in the colonic mucosa (P < 0.05). In the jejunal mucosa, ITAI decreased interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), sIgA and IgG levels together with down-regulation of IFN-γ, TNF-α, MUC2 and ZO-1 mRNA expression (P < 0.05). Furthermore, ITAI decreased IL-10, INF-γ, TNF-α, IgA and IgG concentrations in serum (P < 0.05). Correlation analysis revealed that the change in intestinal microbiota was correlated with alterations of Ig and cytokines.

Conclusions

ITAI affected jejunal and colonic specific bacteria counts, and altered some immune markers levels in the jejunal and colonic mucosa and serum. These findings implicate the potential contribution of hindgut bacteria to immune response in the intestinal mucosa and serum of growing pigs.

Electronic supplementary material

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Effect of Lactobacillus rhamnosus and Bifidobacterium lactis on gingival health, dental plaque, and periodontopathogens in adolescents: a randomised placebo-controlled clinical trial

To determine the effect of a probiotic combination of Lactobacillus rhamnosus GG (LGG) and Bifidobacterium lactis BB-12 on the gingival health, dental plaque accumulation, and the oral carriage of four putative periodontal pathogens in healthy adolescents. 108 schoolboys, aged 13-15 years, participated in this study. They were divided into two groups: probiotics (n=54) and placebo (n=54). Both groups received two probiotic-laced or placebo lozenges twice a day during a four-week period. Plaque Index (PI) and Gingival Index (GI) were recorded at baseline and after four weeks. Salivary and plaque carriage of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum were also monitored likewise. 101 subjects completed the study. A statistically significant reduction in GI was seen in the probiotic group as compared to the placebo group (P=0.012). A reduction in PI was found for both groups, with no difference observed between the groups after intervention (P=0.819). Probiotic lozenges significantly reduced levels of A. actinomycetemcomitans and F. nucleatum in saliva and plaque (P<0.05) and levels of P. gingivalis in plaque (P<0.05), while no significant changes were found in the control group. A significant reduction (P<0.001) was also noted in the total salivary bacterial counts of the test group. The short-term daily consumption of LGG and BB-12 probiotic lozenges improved the gingival health in adolescents and decreased the microbial counts of A. actinomycetemcomitans, and P. gingivalis. Hence probiotic supplements may serve as a simple adjunct to standard oral care for promoting the oral health in adolescents.

Increased Oral Porphyromonas gingivalis Prevalence in Cardiovascular Patients with Uncontrolled Diabetes Mellitus

The aim of this study was to determine the correlation between periodontopathic bacteria and diabetes mellitus (DM) status in cardiovascular disease (CVD) subjects.DM is associated with the progression of periodontitis. Several epidemiological studies have suggested that periodontitis may be a risk factor for CVD. However, no study has compared the periodontal condition between well-controlled and poorly-controlled DM patients with CVD.The subjects were well-controlled (n = 73) or poorly-controlled (n = 39) DM patients with CVD. Blood examinations and dental clinical measurements, including number of teeth, probing pocket depth, bleeding on probing (BOP), and clinical attachment level (CAL) were performed. Periodontopathic bacterial existence was evaluated.Worsened CAL and BOP rate were detected in the uncontrolled DM group compared to the controlled group. We found increased salivary Porphyromonas gingivalis counts in the uncontrolled DM group compared to well-controlled DM subjects.Specific periodontopathic bacterial infection may affect DM condition in CVD patients.

Association of residual feed intake with abundance of ruminal bacteria and biopolymer hydrolyzing enzyme activities during the peripartal period and early lactation in Holstein dairy cows

Background

Residual feed intake (RFI) in dairy cattle typically calculated at peak lactation is a measure of feed efficiency independent of milk production level. The objective of this study was to evaluate differences in ruminal bacteria, biopolymer hydrolyzing enzyme activities, and overall performance between the most- and the least-efficient dairy cows during the peripartal period. Twenty multiparous Holstein dairy cows with daily ad libitum access to a total mixed ration from d − 10 to d 60 relative to the calving date were used. Cows were classified into most-efficient (i.e. with low RFI, n = 10) and least-efficient (i.e. with high RFI, n = 10) based on a linear regression model involving dry matter intake (DMI), fat-corrected milk (FCM), changes in body weight (BW), and metabolic BW.

Results

The most-efficient cows had ~ 2.6 kg/d lower DMI at wk 4, 6, 7, and 8 compared with the least-efficient cows. In addition, the most-efficient cows had greater relative abundance of total ruminal bacterial community during the peripartal period. Compared with the least-efficient cows, the most-efficient cows had 4-fold greater relative abundance of Succinivibrio dextrinosolvens at d − 10 and d 10 around parturition and tended to have greater abundance of Fibrobacter succinogenes and Megaspheara elsdenii. In contrast, the relative abundance of Butyrivibrio proteoclasticus and Streptococcus bovis was lower and Succinimonas amylolytica and Prevotella bryantii tended to be lower in the most-efficient cows around calving. During the peripartal period, the most-efficient cows had lower enzymatic activities of cellulase, amylase, and protease compared with the least-efficient cows.

Conclusions

The results suggest that shifts in ruminal bacteria and digestive enzyme activities during the peripartal period could, at least in part, be part of the mechanism associated with better feed efficiency in dairy cows.

Electronic supplementary material

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The Role of Intestinal C-type Regenerating Islet Derived-3 Lectins for Nonalcoholic Steatohepatitis

C-type regenerating islet derived-3 (Reg3) lectins defend against pathogens and keep commensal bacteria at a distance. Deficiency of Reg3g and Reg3b facilitates alcohol-induced bacterial translocation and alcoholic liver disease. Intestinal Reg3g is down-regulated in animal models of diet-induced obesity, but the functional consequences for nonalcoholic steatohepatitis (NASH) are unknown. The aim of this study was to investigate the role of Reg3 lectins in NASH. NASH was induced by a Western-style fast-food diet in mice deficient for Reg3g or Reg3b and in transgenic mice overexpressing Reg3g in intestinal epithelial cells (Reg3gTg). Glucose tolerance was assessed after 18 weeks and insulin resistance after 19 weeks of feeding. After 20 weeks, mice were assessed for features of the metabolic syndrome. Obesity was not different in genetically modified mice compared with their respective wild-type littermates. Glucose intolerance, liver injury, hepatic inflammation, steatosis, fibrosis, and bacterial translocation to mesenteric lymph nodes and to the liver were not different in Reg3g-deficient mice compared with wild-type littermates. Plasma endotoxin levels were higher in Reg3g-deficient mice. Reg3b deficiency protected against glucose intolerance, but liver disease, bacterial translocation, and plasma endotoxin levels were similar to wild-type littermates. Absence of either REG3G or REG3B protein in the ileum was not compensated for by up-regulation of the respective other REG3 protein. Transgenic Reg3g mice also developed liver injury, steatosis, and fibrosis similar to their wild-type littermates. Conclusion: In contrast to alcoholic liver disease, loss of intestinal Reg3 lectins is not sufficient to aggravate diet-induced obesity and NASH. This supports a multi-hit pathogenesis in NASH. Only glucose metabolism is affected by Reg3b deficiency. (Hepatology Communications 2018;2:393-406).

Abundance of antibiotic resistance genes and bacterial community composition in wild freshwater fish species

This study was aimed to determine the abundance of four antibiotic resistance genes (bla_TEM, ermB, qnrS and sulI), as well as bacterial community composition associated with the intestinal mucus of wild freshwater fish species collected from the Foix and La Llosa del Cavall reservoirs, which represent ecosystems with high and low anthropogenic disturbance, respectively. Water and sediments from these reservoirs were also collected and analyzed to determine the pollution level by antibiotics. The bla_TEM gene was only detected in brown trout and Ebro barbel, which were collected from La Llosa del Cavall reservoir. In contrast, the sulI and qnrS genes were only detected in common carp, which were collected from the Foix reservoir. Although the ermB gene was also detected in common carp, the values were below the limit of quantification. Likewise, water and sediment samples from the Foix reservoir had higher concentrations and more classes of antibiotics than those from La Llosa del Cavall. Pyrosequencing analysis of 16S rRNA genes revealed significant differences in bacterial communities associated with the intestinal mucus of fish species. Therefore, these findings suggest that anthropogenic activities are not only increasing the pollution of aquatic environments, but also contributing to the emergence and spread of antibiotic resistance in organisms that inhabit such environments.

Japanese Cardiovascular Disease Patients with Diabetes Mellitus Suffer Increased Tooth Loss in Comparison to Those without Diabetes Mellitus -A Cross-sectional Study

Objective Tooth loss is an irreversible condition that reflects the end-stage of oral diseases, including periodontitis. Although periodontitis is a major factor in the progression of diabetes mellitus (DM) and cardiovascular disease (CVD), no previous studies have compared tooth loss in CVD patients with and without DM. Methods The subjects included CVD patients with (n=94) and without (n=145) DM who attended Tokyo Medical and Dental University Hospital. Blood examinations and periodontal measurements were performed. Results The oral and periodontal examinations revealed that the numbers of missing teeth in the DM group were increased in comparison to the non-DM group. There was no significant difference between the groups with regard to the incidence of edentulism, the probing pocket depth, the clinical attachment level or the incidence of bleeding on probing. Conclusion We showed that the numbers of missing teeth among CVD patients with DM was significantly higher than that among CVD patients without DM.

Biofilm Formation Plays a Role in the Formation of Multidrug-Resistant Escherichia coli Toward Nutrients in Microcosm Experiments

In this study, microcosms were established to determine the effect of nitrogen (N) and phosphorus (P) on the multidrug resistance and biofilm-forming abilities of Escherichia coli. The expression of biofilm-formation-related genes was detected to establish correlations between genotype and phenotype. Different concentrations of N and P were added to make one control group and four treatment groups. The glass tube method was used to determine biofilm-forming capabilities. Real-time PCR was used to detect the mRNA abundance of six biofilm-formation-related genes in E. coli. No resistant strains were isolated from the control group; meanwhile, multidrug resistance rates were high in the treatment groups. Expression of the biofilm-associated genes luxS, flhD, fliA, motA, and fimH was detected in all treatment groups; however, there was no expression of mqsR. The expression of luxS, flhD, fliA, motA, and fimH significantly correlated with the concentration of N and P, as well as with the appearance and duration of multidrug resistance in different groups. Overall, the results of this study suggest that biofilm-forming ability plays a key role in the formation of multidrug resistance in E. coli after the addition of N and P to a microcosm.

Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis

In this study, it was aimed to determine microbial flora members in three traditional Tulum cheeses (C1, C2 and C3) produced in different villages and settlement areas in İzmir, Turkey. For this purpose, culture depended and 16S rRNA based culture independent methods were used. According to the results of culture depended method, Lactococcus spp., Enterococcus spp., Staphylococcus spp., Lactobacillus spp., Pediococcus spp. and yeast-mold were detected in all samples at different levels. In order to determine and identify both of the culturable and non-culturable microorganisms, denaturing gradient gel electrophoresis (DGGE) method was used. DGGE results have shown that there were eight different dominant microorganisms (Streptococcus thermophilus, Lactococcus lactis subs. lactis, Streptococcus infantarius subs. infantarius, Lactobacillus gallinarum, Streptococcus equinus, Enterococcus faecalis, Enterococcus faecium, Lactococcus garvieae) in three regionally cheese samples. Further more, total bacterial loads were monitored with real-time PCR (qPCR) method. According to the results, 3.5 × 10⁸, 3.8 × 10⁸, 8.4 × 10⁸ copy number of DNA was detected in C1, C2 and C3 cheese samples, respectively. This study is the first description for the dynamics of microbial composition of Izmir Tulum cheese after the production and brining processes.

Effect of Helicobacter pylori infection on chronic periodontitis by the change of microecology and inflammation

Helicobacter pylori (H. pylori), a pathogen inducing peptic disease, is recently found to be binding to the progress of periodontitis. Most previous studies are case-controlled, and they investigate the risk of H. pylori infection in disease the development of while few studies evaluate the correlation between H. pylori and periodontal pathogens. Therefore, we investigated the correlation between H. pylori infection with periodontal parameters, periodontal pathogens and inflammation. The results indicated that patients with H. pylori showed significantly higher probing depth and attachment loss than those without (p < 0.05). Among 28 subgingival plaque samples from 14 patients, the frequencies of Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum and Treponema denticola were significantly higher with H. pylori infection than those without H. pylori infection (p < 0.05). However, the frequency of Aggregatibacter actinomycetemcomitans was lower (p < 0.05). Furthermore, after human acute monocytic leukemia cell line (THP-1) was stimulated with cagA-positive standard strains (cagA⁺ H. pylori 26695), the expression of periodontitis-related molecules Wnt5a, interleukin 8 (IL-8), interleukin 6 (IL-6) and interferon gamma (IFN-γ) significantly increased (p < 0.05). Conversely, the expression of tumor necrosis factor alpha (TNF-α) was almost stable. Meanwhile, cagA⁺ H. pylori promoted significantly higher expression of IL-8 and Wnt5a than isogenic cagA mutants strains (cagA⁻ H. pylori 26695) did. Taken together, our data suggested that H. pylori might promote the growth of some periodontal pathogens and aggravate the progress of chronic periodontitis.

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria

Background

Extensive degradation of amino acids in the rumen via microbial deamination decreases the post-ruminal availability of dietary indispensable amino acids. Together with the normal decrease in voluntary dry matter intake (DMI) around parturition in dairy cows, microbial metabolism contributes to a markedly negative balance of indispensable amino acids, including methionine which may be the first-limiting for milk production. The main objective of the current study was to profile changes in major bacterial species with key functions in cellulose and hemicellulose digestion, xylan breakdown, proteolytic action, propionic acid production, lactate utilization and ruminal biohydrogenation in cows supplemented with rumen-protected Methionine (SM; Smartamine M, Adisseo NA, Alpharetta, GA, USA) from −23 through 30 d relative to parturition. Because ~90% of the methionine in SM bypasses the rumen, ~10% of the methionine is released into the rumen and can be utilized by microbes.

Results

As expected, there was an increase in overall DMI after parturition (Day, P < 0.05) during which cows consumed on average 19.6 kg/d versus 13.9 kg/d in the prepartum period. The postpartum diet contained greater concentrations of lipid and highly-fermentable carbohydrate from corn grain, which likely explains the increases in the relative abundance of Anaerovibrio lipolytica, Megasphaera elsdenii, Prevotella bryantii, Selenomonas ruminantium, Streptococcus bovis, and Succinimonas amylolytica. Despite similar DMI prepartum, cows fed SM had greater (Treatment × Day, P < 0.05) abundance prepartum of Fibrobacter succinogenes, Succinimonas amylolytica, and Succinivibrio dextrinosolvens. However, the greater DMI in cows fed SM after parturition (19.6 kg/d versus 13.9 kg/d) was associated with lower abundance of Fibrobacter succinogenes (2.13 × 10⁻³ versus 2.25 × 10⁻⁴) and Selenomonas ruminantium (2.98 × 10⁻¹ versus 4.10 × 10⁻¹). A lower abundance (Day, P < 0.05) was detected on d 20 compared with d −10 for Fibrobacter succinogenes and Succinivibrio dextrinosolvens. The relative abundance of Butyrivibrio proteoclasticus and Eubacterium ruminantium was stable across treatment and time.

Conclusions

In diets with proper balance of rumen-degradable protein and fermentable carbohydrate, the small fraction of Methionine released from the rumen-protected supplement did not seem to compromise growth of major bacterial species in the rumen. In fact, it had a positive effect on 3 major species prepartum when DMI was similar between groups. Because the actual requirements of Methionine (and Lysine, for example) by the cow during the transition period are unknown, it appears warranted to study the rumen microbiome as it relates to supply of rumen-protected amino acids.

Effects of the citrus flavonoid extract Bioflavex or its pure components on rumen fermentation of intensively reared beef steers

Two experiments were performed to study the effects of the citrus flavonoid extract Bioflavex (BF; Interquim SA, FerrerHealthTech, Sant Cugat, Barcelona, Spain) or its components on the rumen fermentation of a high-concentrate diet. In an in vivo experiment, eight Friesian steers (398 ± 12.2 kg bodyweight) fitted with a rumen cannula were given a basal concentrate (CTR) or a CTR supplemented with BF (450 mg/kg dry matter, DM) in a 2 × 4 crossover design. No differences were observed in performance parameters of BF and CTR steers. Diet BF increased pH values and the molar proportion of propionate and reduced lactate concentration as a result of an increase in the relative abundance of lactate-consuming microorganism Selenomomas ruminantium (P < 0.01) and Megaesphaera elsdenii (P = 0.06). In an in vitro experiment, the effect of BF and its pure flavonoid components added to the incubation medium was studied separately. Bioflavex and its main components naringine, neohesperidine (NH) and poncirine (PC) were added to the incubation medium at 500 µg/g DM, with the unsupplemented substrate also included as a control (CTR). After 12 h of incubation, flavonoid mixture and NH and PC reduced (P < 0.01) the volume of gas produced and the molar proportion of acetate (P < 0.01), and increased that of propionate (P < 0.01). PC reduced the relative quantification of Streptococcus bovis, whereas NH and BF increased the relative quantification of M. elsdenii in relation to CTR (P < 0.01). Bioflavex supplementation in steers in feedlot was effective in preventing a collapse in pH and it enhanced rumen fermentation efficiency through modifying the activity of lactate-consuming bacteria and a greater molar proportion of propionate and a reduction of that of acetate, suggesting its positive role in modulating the activity of rumen microbiota.

Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR

TaqMan and SYBR Green quantitative PCR (qPCR) methods were developed as DNA-based approaches to reproducibly enumerate M13 and T7 phages from phage display selection experiments individually and simultaneously. The genome copies of M13 and T7 phages were quantified by TaqMan or SYBR Green qPCR referenced against M13 and T7 DNA standard curves of known concentrations. TaqMan qPCR was capable of quantifying M13 and T7 phage DNA simultaneously with a detection range of 2.75*10¹-2.75*10⁸genome copies(gc)/μL and 2.66*10¹-2.66*10⁸ genome copies(gc)/μL respectively. TaqMan qPCR demonstrated an efficient amplification efficiency (E_s) of 0.97 and 0.90 for M13 and T7 phage DNA, respectively. SYBR Green qPCR was ten-fold more sensitive than TaqMan qPCR, able to quantify 2.75-2.75*10⁷gc/μL and 2.66*10¹-2.66*10⁷gc/μL of M13 and T7 phage DNA, with an amplification efficiency E_s of 1.06 and 0.78, respectively. Due to its superior sensitivity, SYBR Green qPCR was used to enumerate M13 and T7 phage display clones selected against a cell line, and quantified titers demonstrated accuracy comparable to titers from traditional double-layer plaque assay. Compared to enzyme linked immunosorbent assay, both qPCR methods exhibited increased detection sensitivity and reproducibility. These qPCR methods are reproducible, sensitive, and time-saving to determine their titers and to quantify a large number of phage samples individually or simultaneously, thus avoiding the need for time-intensive double-layer plaque assay. These findings highlight the attractiveness of qPCR for phage enumeration for applications ranging from selection to next-generation sequencing (NGS).

Association of Distinct Fine Specificities of Anti-Citrullinated Peptide Antibodies With Elevated Immune Responses to Prevotella intermedia in a Subgroup of Patients With Rheumatoid Arthritis and Periodontitis

OBJECTIVE

In addition to the long-established link with smoking, periodontitis (PD) is a risk factor for rheumatoid arthritis (RA). This study was undertaken to elucidate the mechanism by which PD could induce antibodies to citrullinated peptides (ACPAs), by examining the antibody response to a novel citrullinated peptide of cytokeratin 13 (CK-13) identified in gingival crevicular fluid (GCF), and comparing the response to 4 other citrullinated peptides in patients with RA who were well-characterized for PD and smoking.

METHODS

The citrullinomes of GCF and periodontal tissue from patients with PD were mapped by mass spectrometry. ACPAs of CK13 (cCK13), tenascin-C (cTNC5), vimentin (cVIM), α-enolase (CEP-1), and fibrinogen β (cFIBβ) were examined by enzyme-linked immunosorbent assay in patients with RA (n = 287) and patients with osteoarthritis (n = 330), and cross-reactivity was assessed by inhibition assays.

RESULTS

A novel citrullinated peptide cCK13-1 (444 TSNASGR-Cit-TSDV-Cit-RP458 ) identified in GCF exhibited elevated antibody responses in RA patients (24%). Anti-cCK13-1 antibody levels correlated with anti-cTNC5 antibody levels, and absorption experiments confirmed this was not due to cross-reactivity. Only anti-cCK13-1 and anti-cTNC5 were associated with antibodies to the periodontal pathogen Prevotella intermedia (P = 0.05 and P = 0.001, respectively), but not with antibodies to Porphyromonas gingivalis arginine gingipains. Levels of antibodies to CEP-1, cFIBβ, and cVIM correlated with each other, and with smoking and shared epitope risk factors in RA.

CONCLUSION

This study identifies 2 groups of ACPA fine specificities associated with different RA risk factors. One is predominantly linked to smoking and shared epitope, and the other links anti-cTNC5 and cCK13-1 to infection with the periodontal pathogen P intermedia.

Detrimental effects of specific Periodontopathic bacterial infection on tachyarrhythmia compared to Bradyarrhythmia

Background

Tachyarrhythmia (TA) and bradyarrhythmia (BA) are cardiac rhythm disorders that result in the decline of quality of life. While patients with periodontitis are at a high risk of cardiovascular disease (CVD), little causal information between TA and BA has been provided to date. To assess the relationship, periodontal bacterial infection in patients with TA or BA was evaluated.

Methods

The subjects were patients with TA (n = 98) or BA (n = 40) who attended Tokyo Medical and Dental University hospital. Periodontal and blood examinations were performed. Periodontopathic bacterial existence in saliva was evaluated.

Results

We found that specific periodontopathic bacteria, Porphyromonas gingivalis and Prevotella intermedia, were highly detected in saliva from TA patients compared to BA subjects. The rates of hypertension and dyslipidemia were comparable between the two groups.

Conclusion

Specific periodontal bacterial infection might affect TA progression.

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

Chronic liver disease is rising in western countries and liver cirrhosis is the 12th leading cause of death worldwide. Simultaneously, use of gastric acid suppressive medications is increasing. Here, we show that proton pump inhibitors promote progression of alcoholic liver disease, non-alcoholic fatty liver disease, and non-alcoholic steatohepatitis in mice by increasing numbers of intestinal Enterococcus spp. Translocating enterococci lead to hepatic inflammation and hepatocyte death. Expansion of intestinal Enterococcus faecalis is sufficient to exacerbate ethanol-induced liver disease in mice. Proton pump inhibitor use increases the risk of developing alcoholic liver disease among alcohol-dependent patients. Reduction of gastric acid secretion therefore appears to promote overgrowth of intestinal Enterococcus, which promotes liver disease, based on data from mouse models and humans. Recent increases in the use of gastric acid-suppressive medications might contribute to the increasing incidence of chronic liver disease.

Proton pump inhibitors (PPIs) reduce gastric acid secretion and modulate gut microbiota composition. Here Llorente et al. show that PPIs induce bacterial overgrowth of enterococci, which, in turn, exacerbate ethanol-induced liver disease both in mice and humans.

Abundance of carbapenemase genes (blaKPC, blaNDM and blaOXA-48) in wastewater effluents from Tunisian hospitals

Carbapenems are β-lactam antibiotics with a broad spectrum of activity and are usually considered the last resort for the treatment of severe infections caused by multidrug-resistant pathogens. The clinically most significant carbapenemases are KPC, NDM, and OXA-48-like enzymes, whose genes have been increasingly reported worldwide in members of the family Enterobacteriaceae. In this study, we quantified the abundance of these genes in wastewater effluents from different Tunisian hospitals. The bla_NDM and bla_OXA-48-like genes were detected at similar concentrations in all hospital wastewater effluents. In contrast, the bla_KPC gene was detected at lower concentration than other genes and it was only detected in three of the seven effluents analyzed. To the best of our knowledge, this study quantified for the first time the abundance of bla_KPC, bla_NDM, and bla_OXA-48-like genes in wastewater effluents from Tunisian hospitals, highlighting the widespread distribution of these carbapenemase genes.

Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection

Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.

Segment-specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs

Despite widespread use of antibiotics for treatment of human diseases and promotion of growth of agricultural animals, our understanding of their effects on the host is still very limited. We used a model in which pigs were fed with or without a cocktail of antibiotics and found, based on the denaturing gradient gel electrophoresis (DGGE) patterns, that the fecal bacteria from the treatment and control animals were distinct. Furthermore, the total bacterial population in the feces tended to be decreased by the antibiotic treatment (P = 0.07), and the counts of Lactobacillus and Clostridium XIVa were significantly reduced (P < 0.05). To explore the effects of antibiotics on host intestinal epithelium, we assessed gene expression profiles of the jejunum and ileum and their response to antibiotic administration. The results indicate that in-feed antibiotics increased expression of genes involved in immune functions in both the jejunum and ileum, some of which were clustered in the coexpression network. Gene ontology terms of metabolic processes were altered predominantly in the jejunum but not in the ileum. Notably, antibiotics diminished intestinal segment-specific transcriptional changes, especially for genes associated with metabolic functions. This study reveals segment-specific responses of host intestinal epithelium to in-feed antibiotics, which can be a valuable resource for deciphering antibiotic-microbiota-host interactions.