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

Dietary supplementation with live or autolyzed yeast: Effects on performance, nutrient digestibility, and ruminal fermentation in dairy cows

This study was conducted to evaluate the effects of live or autolyzed yeast supplementation on dairy cow performance and ruminal fermentation. Two experiments were conducted to evaluate performance, feed sorting, total-tract apparent digestibility of nutrients, purine derivatives excretion, N utilization, ruminal fermentation, and the abundance of specific bacterial groups in the rumen. In experiment 1, 39 Holstein cows (171 ± 40 DIM and 32.6 ± 5.4 kg/d milk yield) were blocked according to parity, DIM, and milk yield and randomly assigned to the following treatments: control (CON); autolyzed yeast fed at 0.625 g/kg DM (AY; Levabon, DSM-Firmenich); or live yeast fed at 0.125 g/kg DM (LY; Vistacell, AB Vista). Cows were submitted to a 2-wk adaptation period followed by a 9-wk trial. In experiment 2, 8 ruminal cannulated Holstein cows (28.4 ± 4.0 kg/d milk yield and 216 ± 30 DIM), of which 4 were multiparous and 4 were primiparous, were blocked according to parity and enrolled into a 4 × 4 Latin square experiment with 21-d periods (the last 7 d for sampling). Cows within blocks were randomly assigned to treatment sequences: control (CON), LY (using the same product and dietary concentration as described in experiment 1), AY, or autolyzed yeast fed at 0.834 g/kg DM (AY2). In experiments 1 and 2, nutrient intake and total-tract apparent digestibility were not affected by treatments. Sorting for long feed particles (>19 mm) tended to be greater in cows fed yeast supplements than CON in experiment 1. Efficiency of N conversion into milk N was increased when feeding yeast supplements in experiment 1, and 3.5% FCM yield tended to be greater in cows fed yeast supplements than CON. Feed efficiency was increased when yeast supplements were fed to cows in relation to CON in experiment 1. In experiment 2, yield of FCM and fat were greater in cows fed yeast supplements compared with CON. Uric acid concentration and output in urine were increased when feeding yeast supplements when compared with CON. Neither ruminal pH nor total VFA were influenced by treatments. The current study did not reveal treatment differences in ruminal abundance of Anaerovibrio lipolytica, the genus Butyrivibrio, Fibrobacter succinogenes, Butyrivibrio proteoclasticus, or Streptococcus bovis. Yeast supplementation can increase feed efficiency without affecting nutrient intake and digestibility, ruminal VFA concentration, or ruminal abundance of specific bacterial groups. Supplementing live or autolyzed yeast, regardless of the dose, resulted in similar performance.

Bacterial DNA and serum IgG antibody titer assays for assessing infection of human-pathogenic and dog-pathogenic Porphyromonas species in dogs

Periodontal disease is highly prevalent in both humans and dogs. Although there have been reports of cross-infection of periodontopathic bacteria, methods for assessing it have yet to be established. The actual status of cross-infection remains to be seen. The purpose of this study was to evaluate the utility of bacterial DNA and serum immunoglobulin G (IgG) antibody titer assays to assess infection of human-pathogenic and dog-pathogenic Porphyromonas species in dogs. Four experimental beagles were used for establishing methods. Sixty-six companion dogs at veterinary clinics visiting for treatment and prophylaxis of periodontal disease were used and divided into healthy, gingivitis, and periodontitis groups. Periodontal pathogens such as Porphyromonas gingivalis and Porphyromonas gulae were investigated as target bacteria. DNA levels of both bacteria were measured using species-specific primers designed for real-time polymerase chain reaction (PCR). Serum IgG titers of both bacteria were measured by enzyme-linked immunosorbent assay (ELISA). PCR primers were confirmed to have high sensitivity and specificity. However, there was no relationship between the amount of bacterial DNA and the severity of the periodontal disease. In addition, dogs with periodontitis had higher IgG titers against both bacteria compared to dogs in the healthy and gingivitis groups; there was cross-reactivity between the two bacteria. Receiver operating characteristic (ROC) analysis of IgG titers against both bacteria showed high sensitivity (>90 %) and specificity (>75 %). Since both bacteria were distinguished by DNA assays, the combination of these assays may be useful in the evaluation of cross-infection.

Perturbed maternal microbiota shapes offspring microbiota during early colonization period in mice

Recent studies have highlighted the impact of disrupted maternal gut microbiota on the colonization of offspring gut microbiota, with implications for offspring developmental trajectories. The extent to which offspring inherit the characteristics of altered maternal gut microbiota remains elusive. In this study, we employed a mouse model where maternal gut microbiota disruption was induced using non-absorbable antibiotics. Systematic chronological analyses of dam fecal samples, offspring luminal content, and offspring gut tissue samples revealed a notable congruence between offspring gut microbiota profiles and those of the perturbed maternal gut microbiota, highlighting the profound influence of maternal microbiota on early-life colonization of offspring gut microbiota. Nonetheless, certain dominant bacterial genera in maternal microbiota did not transfer to the offspring, indicating a bacterial taxonomy-dependent mechanism in the inheritance of maternal gut microbiota. Our results embody the vertical transmission dynamics of disrupted maternal gut microbiota in an animal model, where the gut microbiota of an offspring closely mirrors the gut microbiota of its mother.

Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin

Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.

Comparison of the Effects of Essential Oils from Cannabis sativa and Cannabis indica on Selected Bacteria, Rumen Fermentation, and Methane Production-In Vitro Study

This study aimed to evaluate the effects of essential oils (EOs) extracted from Cannabis sativa L. and Cannabis indica Lam. on in vitro ruminal fermentation characteristics, selected rumen microbial populations, and methane production. GC-MS analyses allowed us to identify 89 compounds in both EOs. It was found that E-β-caryophyllene predominated in C. sativa (18.4%) and C. indica (24.1%). An in vitro (Ankom) test was performed to analyse the control and monensin groups, as well as the 50 µL or 100 µL EOs. The samples for volatile fatty acids (VFAs), lactate, and microbiological analysis were taken before incubation and after 6 and 24 h. The application of EOs of C. indica resulted in an increase in the total VFAs of acetate and propionate after 6 h of incubation. The applied EOs had a greater impact on the reduction in methane production after 6 h, but no apparent effect was noted after 24 h. Lower concentrations of C. sativa and C. indica had a more pronounced effect on Lactobacillus spp. and Buryrivibrio spp. than monensin. The presented findings suggest that C. sativa and C. indica supplementation can modify ruminal fermentation, the concentrations of specific volatile fatty acids, and methane production.

Real-Time PCR Method as Diagnostic Tool for Detection of Periodontal Pathogens in Patients with Periodontitis

The most common type of periodontal disease is chronic periodontitis, an inflammatory condition caused by pathogenic bacteria in subgingival plaque. The aim of our study was the development of a real-time PCR test as a diagnostic tool for the detection and differentiation of five periodontopathogenic bacteria, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, and Treponema denticola, in patients with periodontitis. We compared the results of our in-house method with the micro-IDent® semiquantitative commercially available test based on the PCR hybridization method. DNA was isolated from subgingival plaque samples taken from 50 patients and then analyzed by both methods. Comparing the results of the two methods, they show a specificity of 100% for all bacteria. The sensitivity for A. actinomycetemcomitans was 97.5%, for P. gingivalis 96.88%, and for P. intermedia 95.24%. The sensitivity for Tannerella forsythia and T. denticola was 100%. The Spearman correlation factor of two different measurements was 0.976 for A. actinomycetemcomitans, 0.967 for P. gingivalis, 0.949 for P. intermedia, 0.966 for Tannerella forsythia, and 0.917 for T. denticola. In conclusion, the in-house real-time PCR method developed in our laboratory can provide information about relative amount of five bacterial species present in subgingival plaque in patients with periodontitis. It is likely that such a test could be used in dental diagnostics in assessing the efficacy of any treatment to reduce the bacterial burden.

Phage predation, disease severity, and pathogen genetic diversity in cholera patients

Despite an increasingly detailed picture of the molecular mechanisms of bacteriophage (phage)-bacterial interactions, we lack an understanding of how these interactions evolve and impact disease within patients. In this work, we report a year-long, nationwide study of diarrheal disease patients in Bangladesh. Among cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative polymerase chain reaction while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration depending on resistance mechanisms. In the absence of antiphage defenses, predation was "effective," with a high predator:prey ratio that correlated with increased genetic diversity among the prey. In the presence of antiphage defenses, predation was "ineffective," with a lower predator:prey ratio that correlated with increased genetic diversity among the predators. Phage-bacteria coevolution within patients should therefore be considered in the deployment of phage-based therapies and diagnostics.

Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma

The gut microbiome has been found to play a crucial role in the treatment of multiple myeloma (MM), which is still considered incurable due to drug resistance. In previous studies, we demonstrated that intestinal nitrogen-recycling bacteria are enriched in patients with MM. However, their role in MM relapse remains unclear. This study highlights the specific enrichment of Citrobacter freundii (C. freundii) in patients with relapsed MM. Through fecal microbial transplantation experiments, we demonstrate that C. freundii plays a critical role in inducing drug resistance in MM by increasing levels of circulating ammonium. The ammonium enters MM cells through the transmembrane channel protein SLC12A2, promoting chromosomal instability and drug resistance by stabilizing the NEK2 protein. We show that furosemide sodium, a loop diuretic, downregulates SLC12A2, thereby inhibiting ammonium uptake by MM cells and improving progression-free survival and curative effect scores. These findings provide new therapeutic targets and strategies for the intervention of MM progression and drug resistance.

Evaluation of loop-mediated isothermal amplification method for efficient detection of the periodontopathic bacteria Porphyromonas gingivalis

Background

Periodontitis is a multifactorial, polymicrobial oral inflammatory illness brought on by oral pathogens. Porphyromonas gingivalis is a Gram-negative, obligatory anaerobic, black-pigmented coccobacillus and is regarded as a primary etiological factor in the progression of periodontitis. Rapid, highly senstitive and specific detection methods are emerging. The present study aimed to evaluate the loop-mediated isothermal amplification (LAMP) technique for efficiently detecting P. gingivalis from subgingival plaque samples of chronic periodontitis patients.

Materials and Methods

This study included 50 subgingival plaque samples from patients suffering from chronic periodontitis. The DNA (Deoxyribonucleic acid) was extracted by the "modified proteinase K" method. A set of six primers, targeting the pepO gene of P. gingivalis, was used for conducting LAMP. The amplification was visualized by naked-eye detection and agarose electrophoresis. Conventional polymerase chain reaction (PCR) and real-time qantitative PCR (qPCR) were carried out by targeting the 16SrRNA (16S ribosomal ribonucleic acid) gene of P. gingivalis.

Results

The results showed that LAMP detected P. gingivalis in 40 out of 50 samples (80%). Whereas, qPCR and conventional PCR technique detected P. gingivalis in 38 (76%) and 33 (66%) samples respectively. The sensitivity and specificity of the LAMP method were 94.87% and 90.90%, respectively. With qPCR, the sensitivity and specificity were found to be 92.30% and 81.81%, respectively, whereas, with conventional PCR, it was found to be 76.92% and 72.72%, respectively.

Conclusion

LAMP is an efficient technique for quick, accurate, and reliable identification of P. gingivalis from subgingival plaque samples. The technique needs to be validated analytically, and further studies can be conducted by taking saliva and/or gingival crevicular fluid samples from periodontitis patients.

Investigating the effect of supplementing different levels of Isochrysis galbana on in vitro rumen fermentation parameters

This study aimed to investigate the effect of supplementing Isochrysis galbana (I. galbana) at levels of 0 (control), 1, 2, 3, 4, and 5 (g/100 g DM) of the diet on the gas production kinetics, methane production, rumen fermentation parameters, and relative microbial population in vitro. Supplementation of I. galbana at high level (5 g/100 g DM) caused a significant decrease in total gas production (p < 0.05). High supplementation rates (4 and 5 g/100 g DM) decreased CH4 production relative to the control by 18.4% and 23.2%, respectively. Although rumen ammonia nitrogen (N-NH3) and total volatile fatty acids (VFA) concentrations were affected by dietary treatments, but the VFA profile did not changed. The relative proportion of protozoa and methanogenic archaea as well as Anaerovibrio lipolytica, Prevotella spp., Ruminococcus flavefaciens, and Fibrobacter succinogenes were decreased significantly as a result of microalgae supplementation. However, the relative abundance of Ruminococcus albus, Butyrivibrio fibrisolvens and Selenomonas ruminantium were significantly increased (p < 0.05), related to the control group. As well, the pH was not affected by dietary treatments. It was concluded that I. galbana reduced in vitro CH4 production and methanogenic archaea that its worth to be investigated further in in vivo studies.

Sugar Substitute Stevia Inhibits Biofilm Formation, Exopolysaccharide Production, and Downregulates the Expression of Streptococcal Genes Involved in Exopolysaccharide Synthesis

BACKGROUND

Acid production by sucrose fermentation disturbs the balance in dental plaque by lowering the oral pH. As a consequence of the profound effect of sucrose on caries initiation and progression, many studies have been directed towards finding non-cariogenic artificial sweeteners that can be used as a substitute to sucrose. Existing literature shows that dietary sucrose upregulates the expression of biofilm associated genes involved in exopolysaccharide (EPS) production.

OBJECTIVE

In this study, we aimed to investigate the effect of the sugar substitute stevia on biofilm formation, EPS secretion, and streptococcal genes encoding glucan-binding proteins (Gbps) and glucosyltransferases (Gtfs), which are essential for the synthesis of EPS.

MATERIALS AND METHODS

Streptococcus mutans and Streptococcus gordonii were grown as biofilm cultures with or without stevia and sucrose. Biomass was quantified for biofilm and EPS production by crystal violet staining and the phenol-sulfuric acid method, respectively. Expression of gtfB and gbpB genes was studied by RT-PCR.

RESULTS

The quantities of biofilm were significantly lower when grown in the presence of stevia compared to sucrose in both species (p < 0.05). The proportion of EPS in the biofilm pellet decreased with increasing concentrations of stevia in both species but remained nearly unchanged with sucrose with respect to the control. In both streptococcal species, exposure of stevia decreased the expression of gtfB and gbpB genes compared to sucrose (p < 0.05). In comparison to the untreated control, the expression was decreased in the presence of stevia in both species, while it increased 2.5- to 4-fold in S. mutans and 1.5- to 2.5-fold in S. gordonii in the presence of sucrose.

CONCLUSION

The ability of stevia to inhibit biofilm formation, reduce EPS production, and downregulate the expression of gtfB and gbpB genes in S. mutans and S. gordonii may have potential therapeutic applications in controlling dental plaques and caries.

Quantitative investigation of the bacterial content of periodontal abscess samples by real-time PCR

OBJECTIVES

Periodontal abscesses, which are part of the acute periodontal disease group characterized by the destruction of periodontal tissue with deep periodontal pockets, bleeding on probing, suppuration, and localized pus accumulation, cause rapid destruction of tooth-supporting tissues. This study aimed to evaluate the microbial content of periodontal abscesses by specific and culture-independent qPCR.

METHODS

This study was conducted on 30 volunteers diagnosed with periodontal abscesses and presenting with complaints of localized pain, swelling, and tenderness in the gingiva. Genomic DNA was isolated from the samples taken. Escherichia coli bacteria were used for the standard curve created to calculate the prevalence of target bacteria in the total bacterial load. 16S rRNA Universal primers were used to assess the total bacterial load and prevalence. Bacterial counts were analyzed with Spearman's rank correlation coefficients (ρ) matrix.

RESULTS

From the analysis of Real-Time PCR, Porphyromonas gingivalis (30, 100%), Prevotella intermedia (30, 100%), and Fusobacterium nucleatum (30, 100%) were detected in all samples. Campylobacter rectus (29, 96.6%), Porphyromonas endodontalis (29, 96.6%), Tannerella forsythia (28, 93.3%), Filifactor alocis (28, 93.3%), and Actinomyces naeslundii (28, 93.3%) were also frequently detected.

CONCLUSIONS

Periodontal abscesses were found to be polymicrobial, and not only periodontal pathogens appeared to be associated with the development of periodontal abscesses. The presence, prevalence, and number of Porphyromonas endodontalis and Propionibacterium acnes in the contents of periodontal abscesses were determined for the first time in our study. Further studies are needed to better understand the roles of bacteria in periodontal disease, including abscesses.

The role of NADPH oxidase 1 in alcohol-induced oxidative stress injury of intestinal epithelial cells

Alcohol-mediated reactive oxygen species (ROS) play a vital role in intestinal barrier injury. However, the mechanism of ROS accumulation in enterocytes needs to be explored further. In our study, we found that chronic-binge ethanol-fed mice had increased levels of gut oxidative stress and high intestinal permeability. The transcription profiles of the colonic epithelial cells showed that the level of NADPH oxidase 1 (NOX1) was significantly elevated in alcohol-exposed mice compared with isocaloric-exposed mice. In vitro, NOX1 silencing alleviated ROS accumulation and the apoptosis of human colonic epithelial cells (NCM460), while NOX1 overexpression accelerated oxidative stress injury of NCM460 cells. Propionic acid was reduced in the gut of chronic-binge ethanol-fed mice, compared with isocaloric-fed mice, as observed through untargeted metabolomic analysis. Supplementation with propionate relieved ethanol-induced liver and intestinal barrier injuries and reduced the level of ROS accumulation and apoptosis of ethanol-induced colonic epithelial cells. Propionate alleviating NOX1 induced ROS injury of colonic epithelial cells, independent of G protein-coupled receptors. Propionate significantly inhibited histone deacetylase 2 (HDAC2) expressions both in ethanol-exposed colonic epithelial cells and TNF-α-treated NCM460. Chromatin immunoprecipitation (ChIP) assays showed that propionate suppressed the NOX1 expression by regulating histone acetylation in the gene promoter region. In conclusion, NOX1 induces oxidative stress injury of colonic epithelial cells in alcohol-related liver disease. Propionate, which can act as an endogenous HDAC2 inhibitor, can decrease levels of apoptosis of intestinal epithelial cells caused by oxidative stress.

The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model

From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME® reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.

Sampling and Characterization of Bioaerosols in Poultry Houses

Two poultry Confined Animal Feeding Units (CAFUs), "House A" and "House B", were selected from the TAMU poultry facility for the study, and samples were collected over a five-day period. Bioaerosol sampling was conducted using a Wetted Wall Cyclone (WWC) bioaerosol collector at the two CAFU houses, in which House A housed approximately 720 broiler chickens and roosters, while House B remained unoccupied and served as a reference. Both houses consisted of 24 pens arranged on either side of a central walkway. Bacterial content analysis was conducted using microbial plating, real-time Polymerase Chain Reaction (PCR), and Fatty Acid Methyl Ester (FAME) analysis, while ambient temperature and relative humidity were also monitored. The concentrations of microorganisms in House A showed a highly dynamic range, ranging from 4000 to 60,000 colony forming units (CFU) per cubic meter of air. Second, the WWC samples contained approximately ten-fold more bacterial DNA than the filter samples, suggesting higher levels of viable cells captured by the WWC. Third, significant concentrations of pathogens, including Salmonella, Staphylococcus, and Campylobacter, were detected in the poultry facility. Lastly, the WWC system demonstrated effective functionality and continuous operation, even in the challenging sampling environment of the CAFU. The goal of this study was to characterize the resident population of microorganisms (pathogenic and non-pathogenic) present in the CAFUs and to evaluate the WWC's performance in such an environment characterized by elevated temperature, high dust content, and feathers. This knowledge could then be used to improve understanding microorganism dynamics in CAFUs including the spread of bacterial infections between animals and from animals to humans that work in these facilities, as well as of the WWC performance in this type of environment (elevated temperature, high content of dust and feathers). A more comprehensive understanding can aid in improving the management of bacterial infections in these settings.

Microbial community composition of food waste before anaerobic digestion

Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.

Amino acid digestibility of insect meals and effects on key bacterial groups in excreta of caecectomised laying hens

The chemical composition and amino acids (AA) digestibility were determined in insect meals from mealworms, crickets, black soldier fly (BSF) larvae and BSF prepupae, and soybean meal. Six caecectomised laying hens were individually housed in metabolism cages and fed either a basal diet or one of five assay diets. Diets and hens were arranged in a 6 × 6 Latin square design with 6 subsequent periods. In each period, the laying hens were fed their respective diet for 9 d, and excreta samples were quantitatively collected twice daily from day 5 to 8. On day 9, a sterile plastic bag was attached to the cloaca of each hen to collect excreta for microbiota analysis. The AA digestibility of the insect meals and soybean meal were calculated using a linear regression approach. Crude protein (CP) concentrations in crickets and mealworms were higher than the value in soybean meal, BSF prepupae and BSF larvae. Ether extract concentrations were high in the insect meals and low in the soybean meal. The digestibility of most essential AA in soybean meal was higher (p < 0.05) than in crickets and BSF prepupae and not different from AA digestibility in mealworms and BSF larvae (except for arginine and histidine). The gene copy number of Escherichia coli in excreta from hens fed with BSF prepupae was lower (p < 0.05) than those fed with BSF larvae, whereas the gene copy number of Bacillus spp. and Clostridium spp. in excreta from hens fed with crickets was lower (p < 0.05) than those fed with BSF larvae. In conclusion, the chemical composition and AA digestibility varied among insect meals based on insect species and life stage. The high level of AA digestibility of insect meals supports the assessment that insect meals are a suitable feed component for laying hens, but differences in AA digestibility should be considered in diet formulation.

Multi-omics in vitro study of the salivary modulation of the goat rumen microbiome

Ruminants are able to produce large quantities of saliva which enter into the rumen and salivary components exert different physiological functions. Although previous research has indicated that salivary immunoglobulins can partially modulate the rumen microbial activity, the role of the salivary components other than ions on the rumen microbial ecosystem has not been thoroughly investigated in ruminants. To investigate this modulatory activity, a total of 16 semi-continuous in vitro cultures with oats hay and concentrate were used to incubate rumen fluid from four donor goats with autoclaved saliva (AUT) as negative control, saliva from the same rumen fluid donor (OWN) as positive control, and either goat (GOAT) or sheep (SHEEP) saliva as experimental interventions. Fermentation was monitored throughout 7 days of incubation and the microbiome and metabolome were analysed at the end of this incubation by Next-Generation sequencing and liquid chromatography coupled with mass spectrometry, respectively. Characterisation of the proteome and metabolome of the different salivas used for the incubation showed a high inter-animal variability in terms of metabolites and proteins, including immunoglobulins. Incubation with AUT saliva promoted lower fermentative activity in terms of gas production (-9.4%) and highly divergent prokaryotic community in comparison with other treatments (OWN, GOAT and SHEEP) suggesting a modulatory effect derived from the presence of bioactive salivary components. Microbial alpha-diversity at amplicon sequence variant (ASV) level was unaffected by treatment. However, some differences were found in the microbial communities across treatments, which were mostly caused by a greater abundance of Proteobacteria and Rikenellacea in the AUT treatment and lower of Prevotellaceae. These bacteria, which are key in the rumen metabolism, had greater abundances in GOAT and SHEEP treatments. Incubation with GOAT saliva led to a lower protozoal concentration and propionate molar proportion indicating a capacity to modulate the rumen microbial ecosystem. The metabolomics analysis showed that the AUT samples were clustered apart from the rest indicating different metabolic pathways were promoted in this treatment. These results suggest that specific salivary components contribute to host-associated role in selecting the rumen commensal microbiota and its activity. These findings could open the possibility of developing new strategies to modulate the saliva composition as a way to manipulate the rumen function and activity.

Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment

The gut microbiome influences the pathogenesis and course of metabolic disorders such as diabetes. While it is likely that duodenal mucosa associated microbiota contributes to the genesis and progression of increased blood sugar, including the pre-diabetic stage, it is much less studied than stool. We investigated paired stool and duodenal microbiota in subjects with hyperglycemia (HbA1c ≥ 5.7% and fasting plasma glucose > 100 mg/dl) compared to normoglycemic. We found patients with hyperglycemia (n = 33) had higher duodenal bacterial count (p = 0.008), increased pathobionts and reduction in beneficial flora compared to normoglycemic (n = 21). The microenvironment of duodenum was assessed by measuring oxygen saturation using T-Stat, serum inflammatory markers and zonulin for gut permeability. We observed that bacterial overload was correlated with increased serum zonulin (p = 0.061) and higher TNF-α (p = 0.054). Moreover, reduced oxygen saturation (p = 0.021) and a systemic proinflammatory state [increased total leukocyte count (p = 0.031) and reduced IL-10 (p = 0.015)] characterized the duodenum of hyperglycemic. Unlike stool flora, the variability in duodenal bacterial profile was associated with glycemic status and was predicted by bioinformatic analysis to adversely affect nutrient metabolism. Our findings offer new understanding of the compositional changes in the small intestine bacteria by identifying duodenal dysbiosis and altered local metabolism as potentially early events in hyperglycemia.

In vitro investigation of the impact of contemporary restorative materials on cariogenic bacteria counts and gene expression

OBJECTIVES

The aim of this study was to compare the antibacterial effect of different fluoride-containing and bioactive restorative materials, and their effect on the expression of specific biofilm-associated genes and therefore the caries process.

MATERIALS AND METHODS

The restorative materials utilized in this study included: 1. Filtek Z250, 2. Fuji II LC, 3. Beautifil II, 4. ACTIVA, and 5. Biodentine. For each material, disc-shaped specimens were prepared. The inhibitory effects against Streptococcus mutans, Lactobacillus acidophilus, and Leptotrichia shahii were tested. After incubation for 24 hours and 1 week, colony-forming units (CFUs) were enumerated. From the plates dedicated for biomass quantification and RNA purification, the target glucosyltransferase B (gtfB) and glucan-binding protein B (gbpB) genes were chosen for S. mutans. For L. acidophilus, a gene involved in exopolysaccharide synthesis (epsB) was chosen.

RESULTS

Except for Filtek Z250, all four materials showed statistically significant inhibitory effects on the biofilms of all three species. When biofilms were grown in the presence of the same four materials, the expression of S. mutans gtfB and gbpB genes, was significantly reduced. For L. acidophilus, the decrease in the expression of gtfB gene in the presence of ACTIVA was the highest change seen. The epsB gene expression also decreased. Compared to fluoride-releasing materials, bioactive materials had more inhibitory effect against L. acidophilus, both at 24 hours and 1 week.

CONCLUSIONS

Both fluoride releasing and bioactive materials exhibited a significant inhibitory effect on the biofilm growth. The expression of the targeted biofilm-associated genes was downregulated by both material groups.

CLINICAL SIGNIFICANCE

The findings from this study give insight into the antibacterial effect of fluoride-containing and bioactive materials which would help to reduce the chances for secondary caries and therefore increase the lifetime of dental restorations placed for patients.

Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment

The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.

Modulating phenylalanine metabolism by L. acidophilus alleviates alcohol-related liver disease through enhancing intestinal barrier function

BACKGROUND

Impaired metabolic functions of gut microbiota have been demonstrated in alcohol-related liver disease (ALD), but little is known about changes in phenylalanine metabolism.

METHODS

Bacterial genomics and fecal metabolomics analysis were used to recognize the changes of phenylalanine metabolism and its relationship with intestinal flora. Intestinal barrier function was detected by intestinal alkaline phosphatase (IAP) activity, levels of tight junction protein expression, colonic inflammation and levels of serum LPS. Lactobacillus acidophilus was chosen to correct phenylalanine metabolism of ALD mice by redundancy analysis and Pearson correlation analysis.

RESULTS

Using 16S rRNA sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) methods, we identified elevated levels of phenylalanine and its' metabolites in the gut of alcohol-fed mice compared to control mice and were negatively correlated with the abundance of Lactobacillus, which mainly metabolized phenylalanine. The intestinal phenylalanine level was positively correlated with the colon inflammatory factors TNF-α and IL-6, and negatively correlated with ZO-1 and Occludin. While intestinal alkaline phosphatase (IAP) activity was negatively correlated with the colon inflammatory factors TNF-α, IL-6 and MCP-1, and positively correlated with ZO-1 and Occludin. Increased phenylalanine inhibited IAP activity, blocked LPS dephosphorylation, increased colonic inflammation and bacterial translocation. Phenylalanine supplementation aggravated alcohol-induced liver injury and intestinal barrier dysfunction. Among the 37 Lactobacillus species, the abundance of Lactobacillus acidophilus was most significantly decreased in ALD mice. Supplementation with L. acidophilus recovered phenylalanine metabolism and protected mice from alcohol-induced steatohepatitis.

CONCLUSIONS

Recovery of phenylalanine metabolism through the oral supplementation of L. acidophilus boosted intestinal barrier integrity and ameliorated experimental ALD.

Gut microbiota-derived ursodeoxycholic acid alleviates low birth weight-induced colonic inflammation by enhancing M2 macrophage polarization

BACKGROUND

Low birth weight (LBW) is associated with intestinal inflammation and dysbiosis after birth. However, the underlying mechanism remains largely unknown.

OBJECTIVE

In the present study, we aimed to investigate the metabolism, therapeutic potential, and mechanisms of action of bile acids (BAs) in LBW-induced intestinal inflammation in a piglet model.

METHODS

The fecal microbiome and BA profile between LBW and normal birth weight (NBW) neonatal piglets were compared. Fecal microbiota transplantation (FMT) was employed to further confirm the linkage between microbial BA metabolism and intestinal inflammation. The therapeutic potential of ursodeoxycholic acid (UDCA), a highly differentially abundant BA between LBW and NBW piglets, in alleviating colonic inflammation was evaluated in both LBW piglets, an LBW-FMT mice model, and a DSS-induced colitis mouse model. The underlying cellular and molecular mechanisms by which UDCA suppresses intestinal inflammation were also investigated in both DSS-treated mice and a macrophage cell line. Microbiomes were analyzed by using 16S ribosomal RNA sequencing. Fecal and intestinal BA profiles were measured by using targeted BA metabolomics. Levels of farnesoid X receptor (FXR) were knocked down in J774A.1 cells with small interfering RNAs.

RESULTS

We show a significant difference in both the fecal microbiome and BA profiles between LBW and normal birth weight animals in a piglet model. Transplantation of the microbiota of LBW piglets to antibiotic-treated mice leads to intestinal inflammation. Importantly, oral administration of UDCA, a major BA diminished in the intestinal tract of LBW piglets, markedly alleviates intestinal inflammation in LBW piglets, an LBW-FMT mice model, and a mouse model of colitis by inducing M2 macrophage polarization. Mechanistically, UDCA reduces inflammatory cytokine production by engaging BA receptor FXR while suppressing NF-κB activation in macrophages.

CONCLUSIONS

These findings establish a causal relationship between LBW-associated intestinal abnormalities and dysbiosis, suggesting that restoring intestinal health and postnatal maldevelopment of LBW infants may be achieved by targeting intestinal microbiota and BA metabolism. Video Abstract.

Temporary establishment of bacteria from indoor plant leaves and soil on human skin

BACKGROUND

Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing.

RESULTS

Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing.

CONCLUSIONS

This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.

The Role of Histo-Blood Group Antigens and Microbiota in Human Norovirus Replication in Zebrafish Larvae

Human norovirus (HuNoV) is the major agent for viral gastroenteritis, causing >700 million infections yearly. Fucose-containing carbohydrates named histo-blood group antigens (HBGAs) are known (co)receptors for HuNoV. Moreover, bacteria of the gut microbiota expressing HBGA-like structures have shown an enhancing effect on HuNoV replication in an in vitro model. Here, we studied the role of HBGAs and the host microbiota during HuNoV infection in zebrafish larvae. Using whole-mount immunohistochemistry, we visualized the fucose expression in the zebrafish gut for the HBGA Lewis X [Le^X, α(1,3)-fucose] and core fucose [α(1,6)-fucose]. Costaining of HuNoV-infected larvae proved colocalization of Le^X and to a lower extent core fucose with the viral capsid protein VP1, indicating the presence of fucose residues on infected cells. Upon blocking of fucose expression by a fluorinated fucose analogue, HuNoV replication was strongly reduced. Furthermore, by comparing HuNoV replication in conventional and germfree zebrafish larvae, we found that the natural zebrafish microbiome does not have an effect on HuNoV replication, contrary to earlier reports about the human gut microbiome. Interestingly, monoassociation with the HBGA-expressing Enterobacter cloacae resulted in a minor decrease in HuNoV replication, which was not triggered by a stronger innate immune response. Overall, we show here that fucose has an essential role for HuNoV infection in zebrafish larvae, as in the human host, but their natural gut microbiome does not affect viral replication. IMPORTANCE Despite causing over 700 million infections yearly, many gaps remain in the knowledge of human norovirus (HuNoV) biology due to an historical lack of efficient cultivation systems. Fucose-containing carbohydrate structures, named histo-blood group antigens, are known to be important (co)receptors for viral entry in humans, while the natural gut microbiota is suggested to enhance viral replication. This study shows a conserved mechanism of entry for HuNoV in the novel zebrafish infection model, highlighting the pivotal opportunity this model represents to study entry mechanisms and identify the cellular receptor of HuNoV. Our results shed light on the interaction of HuNoV with the zebrafish microbiota, contributing to the understanding of the interplay between gut microbiota and enteric viruses. The ease of generating germfree animals that can be colonized with human gut bacteria is an additional advantage of using zebrafish larvae in virology. This small animal model constitutes an innovative alternative to high-severity animal models.

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

Microbial community in resistant and susceptible Churra sheep infected by Teladorsagia circumcincta

Gastrointestinal nematodes (GIN) are a major threat to health and welfare in small ruminants worldwide. Teladorsagia circumcincta is a nematode that inhabits the abomasum of sheep, especially in temperate regions, causing important economic losses. Given that T. circumcincta and microbiome share the same niche, interactions between them and the host are expected. Although it is known that within a sheep breed there are animals that are more resistant than others to infection by GIN, it is not known if the microbiome influences the phenotype of these animals. Under this condition, 12 sheep were classified according to their cumulative faecal egg count (cFEC) at the end of a first experimental infection, 6 as resistant group (RG) and 6 as susceptible group (SG) to T. circumcincta infection. Then, all sheep were experimentally infected with 70,000 L3 of T. circumcincta and at day 7 days post-infection were euthanized. At necropsy, gastric mucosa and gastric content from abomasum were collected to extract bacterial DNA and sequence V3-V4 region from 16S rRNA gene using Ilumina technology. After bioanalysis performed, results showed that α-diversity and β-diversity remained similar in both groups. However, resistant phenotype sheep showed a higher number of bacteria butyrate-fermenting species as Clostridium sensu stricto 1 (abundance in RG: 1.29% and in SG: 0.069%; p = 0.05), and Turicibacter (abundance in RG: 0.31% and in SG: 0.027%; p = 0.07) in gastric content but also Serratia spp in gastric mucosa (abundance in RG: 0.12% and in SG: 0.041%; p = 0.07). A trend towards a significant negative correlation between cFEC and Clostridium sensu stricto 1 abundance in gastric content was detected (r = - 0.537; p = 0.08). These data suggest that microbiome composition could be another factor associated with the development of the resistant phenotype modifying the interaction with the host and the in last instance affecting the individual risk of infection.

Effect of Sodium Nitrate and Cysteamine on In Vitro Ruminal Fermentation, Amino Acid Metabolism and Microbiota in Buffalo

Nitrate is used as a methane inhibitor while cysteamine is considered as a growth promoter in ruminants. The present study evaluated the effect of sodium nitrate and cysteamine on methane (CH4) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. Four treatments containing a 0.5 g of substrate were supplemented with 1 mg/mL sodium nitrate (SN), 100 ppm cysteamine hydrochloride (CS), and a combination of SN 1 mg/mL and CS 100 ppm (CS+SN), and a control (no additive) were applied in a completely randomized design. Each treatment group had five replicates. Two experimental runs using in vitro batch culture technique were performed for two consecutive weeks. Total gas and CH4 production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, and 72 h of incubation. The results showed that SN and CS+SN reduced the production of total gas and CH4, increased the rumen pH, acetate, acetate to propionate ratio (A/P), and microbial protein (MCP) contents (p < 0.05), but decreased other volatile fatty acids (VFA) and total VFA (p = 0.001). The CS had no effect on CH4 production and rumen fermentation parameters except for increasing A/P. The CSN increased the populations of total bacteria, fungi, and methanogens but decreased the diversity and richness of rumen microorganisms. In conclusion, CS+SN exhibited a positive effect on rumen fermentation by increasing the number of fiber degrading and hydrogen-utilizing bacteria, with a desirable impact on rumen fermentation while reducing total gas and CH4 production.

Active Dry Yeast and Thiamine in Synergistic Mode Can Mitigate Adverse Effects of In Vitro Ruminal Acidosis Model of Goats

Ruminal acidosis is a type of metabolic disorder of high-yielding ruminants which is associated with the consumption of a high-grain diet. It not only harms the productive efficiency, health and wellbeing of the animals but also has detrimental effects on the economy of the farmers. Various strategies have been adapted to control ruminal acidosis. However, none of them have produced the desired results. This research was carried out to investigate the potential of active dry yeast (ADY) and thiamine in a synergistic mode to mitigate in vitro-induced ruminal acidosis. The purpose of this study was to determine how active dry yeast alone and in combination with thiamine affected the ruminal pH, lactate, volatile fatty acids, lipopolysaccharides (LPS) and microbial community in in vitro-induced ruminal acidosis. The experiment comprises three treatment groups, (1) SARA/control, (2) ADY and (3) ADYT (ADY + thiamine). In vitro batch fermentation was conducted for 24 h. The results indicated that ruminal induced successfully and both additives improved the final pH (p < 0.01) and decreased the LPS and lactate (p < 0.01) level as compared to the SARA group. However, the ADYT group decreased the level of lactate below 0.5 mmol/L. Concomitant to fermentation indicators, both the treatment groups decreased (p < 0.05) the abundance of lactate-producing bacteria while enhancing (p < 0.01) the abundance of lactate-utilizing bacteria. However, ADYT also increased (p < 0.05) the abundance of protozoa compared to the SARA and ADY group. Therefore, it can be concluded that ADY and thiamine in synergistic mode could be a better strategy in combating the adverse effects of subacute ruminal acidosis.

mbtD and celA1 association with ethambutol resistance in Mycobacterium tuberculosis: A multiomics analysis

Ethambutol (EMB) is a first-line antituberculosis drug currently being used clinically to treat tuberculosis. Mutations in the embCAB operon are responsible for EMB resistance. However, the discrepancies between genotypic and phenotypic EMB resistance have attracted much attention. We induced EMB resistance in Mycobacterium tuberculosis in vitro and used an integrated genome–methylome–transcriptome–proteome approach to study the microevolutionary mechanism of EMB resistance. We identified 509 aberrantly methylated genes (313 hypermethylated genes and 196 hypomethylated genes). Moreover, some hypermethylated and hypomethylated genes were identified using RNA-seq profiling. Correlation analysis revealed that the differential methylation of genes was negatively correlated with transcription levels in EMB-resistant strains. Additionally, two hypermethylated candidate genes (mbtD and celA1) were screened by iTRAQ-based quantitative proteomics analysis, verified by qPCR, and corresponded with DNA methylation differences. This is the first report that identifies EMB resistance-related genes in laboratory-induced mono-EMB-resistant M. tuberculosis using multi-omics profiling. Understanding the epigenetic features associated with EMB resistance may provide new insights into the underlying molecular mechanisms.

Intestinal Klebsiella pneumoniae Contributes to Pneumonia by Synthesizing Glutamine in Multiple Myeloma

Pneumonia accounts for a significant cause of morbidity and mortality in multiple myeloma (MM) patients. It has been previously shown that intestinal Klebsiella pneumonia (K. pneumonia) enriches in MM and promotes MM progression. However, what role the altered gut microbiota plays in MM with pneumonia remains unknown. Here, we show that intestinal K. pneumonia is significantly enriched in MM with pneumonia. This enriched intestinal K. pneumonia links to the incidence of pneumonia in MM, and intestinal colonization of K. pneumonia contributes to pneumonia in a 5TGM1 MM mice model. Further targeted metabolomic assays reveal the elevated level of glutamine, which is consistently increased with the enrichment of K. pneumonia in MM mice and patients, is synthesized by K. pneumonia, and leads to the elevated secretion of TNF-α in the lung normal fibroblast cells for the higher incidence of pneumonia. Inhibiting glutamine synthesis by establishing glnA-mutated K. pneumonia alleviates the incidence of pneumonia in the 5TGM1 MM mice model. Overall, our work proposes that intestinal K. pneumonia indirectly contributes to pneumonia in MM by synthesizing glutamine. Altogether, we unveil a gut–lung axis in MM with pneumonia and establish a novel mechanism and a possible intervention strategy for MM with pneumonia.

Microbiome Changes During Regenerative Endodontic Treatment Using Different Methods of Disinfection

INTRODUCTION

The purpose of this study was to characterize qualitatively and quantitatively the changes in the endodontic microbiome, in teeth with necrotic pulp, open apexes and apical periodontitis, with three antimicrobial protocols, undertaken in a multicenter clinical trial.

METHODS

Microbiological samples were collected from 116 RET teeth, and 97 qualified for inclusion. The teeth were randomly divided into three treatment groups: apexification (APEX), regeneration (REGEN) and revascularization (REVASC), all in two appointments. The group variables in the first appointment irrigants, and second appointment irrigants and medicaments were as follows: APEX: 5.25-6% NaOCl, 5.25-6% NaOCl + 17% EDTA and calcium hydroxide; REGEN: 1.25% NaOCl, 17% EDTA and 0.1 mg/mL triple antibiotic paste (TAP); and REVASC 5.25% NaOCl, saline and 1g/mL TAP, respectively. Sampling was done upon access (S0), after irrigation in the first appointment (S1), and after using medication and irrigation in the second appointment (S2).

RESULTS

Quantitative PCR analysis of the 16S rRNA gene showed significant reduction in bacterial load from S0 to S2 in all groups; however, the APEX and REVASC groups had significantly less residual DNA than the REGEN group (p=0.0045). The relative abundance of Bacteroidetes, Fusobacteria, Spirochaetes and Synergistetes were reduced with the treatment rendered. However, relative abundance of Firmicutes and Actinobacteria was not changed, and that of Proteobacteria increased. LEfSe analysis showed that reduction in bacterial taxa was more in REVASC than APEX which in turn was more than in REGEN.

CONCLUSION

Enhanced antimicrobial protocols lead to better reduction in quantitative and qualitative parameters of the endodontic microflora.

Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields

Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4⁺ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4⁺ T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.

Residual feed intake in peripartal dairy cows is associated with differences in milk fat yield, ruminal bacteria, biopolymer hydrolyzing enzymes, and circulating biomarkers of immunometabolism

Residual feed intake (RFI) measures feed efficiency independent of milk production level, and is typically calculated using data past peak lactation. In the current study, we retrospectively classified multiparous Holstein cows (n = 320) from 5 of our published studies into most feed-efficient (M-eff) or least feed-efficient (L-eff) groups using performance data collected during the peripartal period. Objectives were to assess differences in profiles of plasma biomarkers of immunometabolism, relative abundance of key ruminal bacteria, and activities of digestive enzymes in ruminal digesta between M-eff and L-eff cows. Individual data from cows with ad libitum access to a total mixed ration from d -28 to d +28 relative to calving were used. A linear regression model including dry matter intake (DMI), energy-corrected milk (ECM), changes in body weight (BW), and metabolic BW was used to classify cows based on RFI divergence into L-eff (n = 158) and M-eff (n = 162). Plasma collected from the coccygeal vessel at various times around parturition (L-eff = 60 cows; M-eff = 47 cows) was used for analyses of 30 biomarkers of immunometabolism. Ruminal digesta collected via esophageal tube (L-eff = 19 cows; M-eff = 29 cows) was used for DNA extraction and assessment of relative abundance (%) of 17 major bacteria using real-time PCR, as well as activity of cellulase, amylase, xylanase, and protease. The UNIVARIATE procedure of SAS 9.4 (SAS Institute Inc.) was used for analyses of RFI coefficients. The MIXED procedure of SAS was used for repeated measures analysis of performance, milk yield and composition, plasma immunometabolic biomarkers, ruminal bacteria, and enzyme activities. The M-eff cows consumed less DMI during the peripartal period compared with L-eff cows. In the larger cohort of cows, despite greater overall BW for M-eff cows especially in the prepartum (788 vs. 764 kg), no difference in body condition score was detected due to RFI or the interaction of RFI × time. Milk fat content (4.14 vs. 3.75 ± 0.06%) and milk fat yield (1.75 vs. 1.62 ± 0.04 kg) were greater in M-eff cows. Although cumulative ECM yield did not differ due to RFI (1,138 vs. 1,091 ± 21 kg), an RFI × time interaction due to greater ECM yield was found in M-eff cows. Among plasma biomarkers studied, concentrations of nonesterified fatty acids, β-hydroxybutyrate, bilirubin, ceruloplasmin, haptoglobin, myeloperoxidase, and reactive oxygen metabolites were overall greater, and glucose, paraoxonase, and IL-6 were lower in M-eff compared with L-eff cows. Among bacteria studied, abundance of Ruminobacter amylophilus and Prevotella ruminicola were more than 2-fold greater in M-eff cows. Despite lower ruminal activity of amylase in M-eff cows in the prepartum, regardless of RFI, we observed a marked linear increase after calving in amylase, cellulase, and xylanase activities. Protease activity did not differ due to RFI, time, or RFI × time. Despite greater concentrations of biomarkers reflective of negative energy balance and inflammation, higher feed efficiency measured as RFI in peripartal dairy cows might be associated with shifts in ruminal bacteria and amylase enzyme activity. Further studies could help address such factors, including the roles of the liver and the mammary gland.

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women

Background

The establishment of symbiotic microbiota in pregnant women is important for both the mother and her offspring. Little is known about the salivary symbiotic bacteria in pregnancy, and analysis of composition of microbiome (ANCOM) is useful to detect small differences in the number of bacteria. The aim of this study was to investigate the differences in the salivary bacteria between healthy pregnant and non-pregnant women using ANCOM.

Methods

Unstimulated saliva samples were collected from 35 healthy pregnant women at 35 weeks gestation and 30 healthy non-pregnant women during menstruation. All participants underwent a periodontal examination. Estradiol and progesterone levels were examined by enzyme-linked immunosorbent assay. DNA extracted from the saliva was assessed by 16S ribosomal RNA amplicon sequencing and real-time PCR.

Results

Salivary estradiol and progesterone levels were significantly increased in pregnant women. The alpha and beta diversities were higher in pregnant women than in non-pregnant women. The largest effect size difference noted when the microbiota of the pregnant and non-pregnant women were analyzed was that for Bifidobacteriales. Levels of Bifidobacterium dentium, but not of Bifidobacterium adolescentis, were significantly increased in pregnant women, and the levels were significantly correlated with progesterone concentration.

Conclusion

The results suggest that Bifidobacterium and progesterone levels are elevated in the saliva of healthy pregnant women compared with non-pregnant women.

Increased acrolein-DNA adducts in buccal brushings of e-cigarette users

DNA adducts are central in the mechanism of carcinogenesis by genotoxic agents. We compared levels of a DNA adduct of acrolein, a genotoxic carcinogen found in e-cigarette vapor, in oral cell DNA of e-cigarette users and non-users of any tobacco or nicotine product. e-Cigarette users and non-users visited our clinic once monthly for 6 months, and oral brushings and urine samples were collected. For this study, we analyzed oral cell DNA adducts from three monthly visits in e-cigarette users and non-users as confirmed by urinary cyanoethyl mercapturic acid and total nicotine equivalents. DNA was isolated from the oral brushings and analyzed by a validated liquid chromatography-nanoelectrospray ionization-high resolution tandem mass spectrometry method for the acrolein DNA adduct 8R/S-3-(2'-deoxyribos-1'-yl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a]purine-10-(3H)-one (γ-OH-Acr-dGuo). The median value of this DNA adduct in the e-cigarette users was 179 fmol/µmol dGuo (range 5.0 - 793 fmol/µmol dGuo) while that for non-users was 21.0 fmol/µmol dGuo (range 5.0 - 539 fmol/µmol dGuo), P = 0.001. These results demonstrate for the first time that e-cigarette users have elevated levels of a carcinogen-DNA adduct in their oral cells.

The Effect of Benzyl Isothiocyanate on the Expression of Genes Encoding NADH Oxidase and Fibronectin-Binding Protein in Oral Streptococcal Biofilms

Recent studies have shown that antimicrobial treatment results in up- or down regulation of several virulence-associated genes in bacterial biofilms. The genes encoding NADH oxidase (nox) and fibronectin-binding protein (fbp) are known to play important roles in biofilm growth of some oral bacterial species. The objective was to study the effect of benzyl isothiocyanate (BITC), an antimicrobial agent from Miswak plant, on the expression of nox and fbp genes in some oral streptococci. The biofilms were treated with BITC and mRNA expression of nox and fbp genes was measured by comparative ΔΔCt method. The highest amount of biofilm mass was produced by A. defectiva, followed by S. gordonii, S. mutans, G. elegans and G. adiacens. Upon treatment with BITC, S. gordonii biofilms showed highest folds change in mRNA expression for both fbp and nox genes followed by S. mutans, A. defectiva, and G. adiacens. G. elegans mRNA levels for nox were extremely low. In conclusion, BITC treatment of the biofilms caused an upregulation of biofilm-associated genes fbp and nox genes in most of the tested species suggesting the significance of these genes in biofilm lifestyle of these oral bacteria and needs further investigation to understand if it contributes to antimicrobial resistance.

An optimized approach for processing of frozen lung and lavage samples for microbiome studies

The respiratory tract has a resident microbiome with low biomass and limited diversity. This results in difficulties with sample preparation for sequencing due to uneven bacteria-to-host DNA ratio, especially for small tissue samples such as mouse lungs. We compared effectiveness of current procedures used for DNA extraction in microbiome studies. Bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected to test different forms of sample pre-treatment and extraction methods to increase bacterial DNA yield and optimize library preparation. DNA extraction using a pre-treatment method of mechanical lysis (lung tissue) and one-step centrifugation (BALF) increased DNA yield and bacterial content of samples. In contrast, a significant increase of environmental contamination was detected after phenol chloroform isoamyl alcohol (PCI) extraction and nested PCR. While PCI has been a standard procedure used in microbiome studies, our data suggests that it is not efficient for DNA extraction of frozen low biomass samples. Finally, a DNA Enrichment kit was tested and found to improve the 16S copy number of lung tissue with a minor shift in microbial composition. Overall, we present a standardized method to provide high yielding DNA and improve sequencing coverage of low microbial biomass frozen samples with minimal contamination.

Lactobacillus helveticus Prevents Periodontitis Induced by Aggregatibacter actinomycetemcomitans in Rats by Regulating β-Defensins

Objective

To study the preventive effect of Lactobacillus helveticus (L. helveticus) on periodontitis induced by Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) in rats.

Methods

Eighteen 8-week-old female rats were randomly divided into three groups: Sham group, Trehalose group, and L. helveticus SBT2171 (LH2171) group. We measured the distance of the cementoenamel junction-alveolar bone crest (CEJ-ABC) to evaluate alveolar bone resorption. Hematoxylin-eosin staining was used to observe the histopathological changes of rat hemimaxillary tissues. We detected the expression of β-defensins, tumor necrosis factor-α (TNF-α), interleukin- (IL-) 1β, and IL-6 and the number of A. actinomycetemcomitans in rat gingival tissues by quantitative reverse transcriptase polymerase chain reaction. The levels of IL-1β, IL-6, and TNF-α in rat gingival tissues were also measured by enzyme-linked immunosorbent assay.

Results

Compared with the Trehalose group, the distance of CEJ-ABC was prominently reduced and alveolar bone resorption was notably improved in the LH2171 group. And the infiltration of inflammatory cells in the hemimaxillary tissue decreased obviously, periodontal fibers were arranged neatly, connective tissue small blood vessels proliferated, and the number of A. actinomycetemcomitans reduced significantly in the LH2171 group. In addition, the mRNA expression and release of inflammatory factors in the gingival tissues in the LH2171 group were notably lower than those in the Trehalose group. On the 21st and 36th day, the expression of β-defensins in the gingival tissue of the LH2171 group increased significantly.

Conclusion

L. helveticus improves alveolar bone resorption and increases the expression of β-defensins thereby inhibiting the number of A. actinomycetemcomitans and thus prevents periodontitis.

Intrahepatic microbes govern liver immunity by programming NKT cells

The gut microbiome shapes local and systemic immunity. The liver is presumed to be a protected sterile site. As such, a hepatic microbiome has not been examined. Here, we showed a liver microbiome in mice and humans that is distinct from the gut and is enriched in Proteobacteria. It undergoes dynamic alterations with age and is influenced by the environment and host physiology. Fecal microbial transfer experiments revealed that the liver microbiome is populated from the gut in a highly selective manner. Hepatic immunity is dependent on the microbiome, specifically Bacteroidetes species. Targeting Bacteroidetes with oral antibiotics reduced hepatic immune cells by ~90%, prevented APC maturation, and mitigated adaptive immunity. Mechanistically, our findings are consistent with presentation of Bacteroidetes-derived glycosphingolipids to NKT cells promoting CCL5 signaling, which drives hepatic leukocyte expansion and activation, among other possible host-microbe interactions. Collectively, we reveal a microbial - glycosphingolipid - NKT - CCL5 axis that underlies hepatic immunity.

Enhancing production of herpes simplex virus type 1 in oral epithelial cells by co-infection with Aggregatibacter actinomycetemcomitans

BACKGROUND/PURPOSE

The association between herpetic/bacterial co-infection and periodontal diseases has been reported. However, how interactions between herpesviruses and periodontal bacteria dampen periodontal inflammation is still unclear. This study determined effects of co-infection with oral bacteria, including Streptococcus sanguinis, Fusobacterium nucleatum or Aggregatibacter actinomycetemcomitans, in herpes simplex virus type 1 (HSV-1)-infected oral epithelial cells.

METHODS

Cell viability was determined by detection the activity of mitochondrial dehydrogenase. Viral production was measured using the plaque assay. Levels of bacterial and viral DNA were determined by real-time polymerase chain reaction. Secretion of interleukin (IL)-6 and IL-8 was measured using the enzyme-linked immunosorbent assay.

RESULTS

Viability was not further reduced by bacterial co-infection in HSV-1-infected cells. Co-infection with HSV-1 and S. sanguinis or F. nucleatum reduced the viral yield whereas co-infection with HSV-1 and A. actinomycetemcomitans significantly enhanced the viral yield in oral epithelial cells. The enhancing effect of A. actinomycetemcomitans was not affected by bacterial heat-inactivation. Co-infection with HSV-1/A. actinomycetemcomitans increased intracellular levels of both viral and bacterial DNA. Secretion of IL-6 and IL-8 stimulated by A. actinomycetemcomitans infection was partly reduced by co-infection with HSV-1 in oral epithelial cells.

CONCLUSION

In contrast to S. sanguinis and F. nucleatum, A. actinomycetemcomitans enhanced the yield of HSV-1. Either HSV-1 or A. actinomycetemcomitans may be benefited from co-infection, in aspects of increases in production of viral and bacterial DNA as well as reductions in cytokine secretion. These findings echoed with previous clinical studies showing co-infection of HSV and A. actinomycetemcomitans in patients with aggressive periodontitis.

Periodontal Infection Aggravates C1q-Mediated Microglial Activation and Synapse Pruning in Alzheimer's Mice

Periodontitis is a dysbiotic infectious disease that leads to the destruction of tooth supporting tissues. There is increasing evidence that periodontitis may affect the development and severity of Alzheimer's disease (AD). However, the mechanism(s) by which periodontal infection impacts the neurodegenerative process in AD remains unclear. In the present study, using an amyloid precursor protein (APP) knock-in (App KI) AD mouse model, we showed that oral infection with Porphyromonas gingivalis (Pg), a keystone pathogen of periodontitis, worsened behavioral and cognitive impairment and accelerated amyloid beta (Aβ) accumulation in AD mice, thus unquestionably and significantly aggravating AD. We also provide new evidence that the neuroinflammatory status established by AD, is greatly complicated by periodontal infection and the consequential entry of Pg into the brain via Aβ-primed microglial activation, and that Pg-induced brain overactivation of complement C1q is critical for periodontitis-associated acceleration of AD progression by amplifying microglial activation, neuroinflammation, and tagging synapses for microglial engulfment. Our study renders support for the importance of periodontal infection in the innate immune regulation of AD and the possibility of targeting microbial etiology and periodontal treatment to ameliorate the clinical manifestation of AD and lower AD prevalence.

Responsive changes of rumen microbiome and metabolome in dairy cows with different susceptibility to subacute ruminal acidosis

Subacute ruminal acidosis (SARA) represents one of the most important digestive disorders in intensive dairy farms, and dairy cows are individually different in the severity of SARA risk. The objectives of the current study were to investigate differences in the ruminal bacterial community and metabolome in dairy cattle with different susceptibility to SARA. In the present study, 12 cows were initially enrolled in the experiment. Based on average ruminal pH, 4 cows with the lowest ruminal pH were assigned to the susceptible group (SUS, pH = 5.76, n = 4) and 4 cows with the highest ruminal pH assigned to the tolerant group (TOL, pH = 6.10, n = 4). Rumen contents from susceptible (SUS, n = 4) and tolerant (TOL, n = 4) dairy cows were collected through rumen fistula to systematically reveal the rumen microbial and metabolic alterations of dairy cows with different susceptibility to SARA using multi-omics approaches (16S and 18S rRNA gene sequencing and metabolome). The results showed that despite being fed the same diet, SUS cows had lower ruminal pH and higher concentrations of total volatile fatty acids (VFA) and propionate than TOL cows (P < 0.05). No significant differences were observed in dry matter intake, milk yield, and other milk compositions between the SUS and TOL groups (P > 0.05). The principal coordinates analysis based on the analysis of molecular variance indicated a significant difference in bacterial composition between the two groups (P = 0.01). More specifically, the relative abundance of starch-degrading bacteria (Prevotella spp.) was greater (P < 0.05), while the proportion of fiber-degrading bacteria (unclassified Ruminococcaceae spp., Ruminococcus spp., Papillibacter, and unclassified Family_XIII) was lower in the rumen of SUS cows compared with TOL cows (P < 0.05). Community analysis of protozoa showed that there were no significant differences in the diversity, richness, and community structure (P > 0.05). Metabolomics analysis revealed that the concentrations of organic acids (such as lactic acid), biogenic amines (such as histamine), and bacterial degradation products (such as hypoxanthine) were significantly higher in the SUS group compared to the TOL group (P < 0.05). These findings revealed that the higher proportion of starch-degrading bacteria/lower fiber-degrading bacteria in the rumen of SUS cows resulted in higher VFA-producing capacity, in particular propionate. This caused a disruption in metabolic homeostasis in the rumen which might be the reason for the higher susceptibility to SARA. Overall, these findings enhanced our understanding of the ruminal microbiome and metabolic changes in cows susceptible to SARA.

Bulik C, Carroll IM. Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice

Anorexia nervosa (AN) is a psychiatric disorder that presents with profound weight dysregulation, metabolic disturbances, and an abnormal composition of gut microbial communities. As the intestinal microbiota can influence host metabolism, the impact of enteric microbial communities from patients with AN on host weight and adiposity was investigated. Germ-free (GF) mice were colonized with fecal microbiotas from either patients with AN (n = 4) prior to inpatient treatment (AN T1, n = 50 recipient mice), the same 4 patients following clinical renourishment (AN T2, n = 53 recipient mice), or age- and sex-matched non-AN controls (n = 4 human donors; non-AN, n = 50 recipient mice). Biological and fecal microbiota data were analyzed with linear mixed-effects models. Body weight did not differ significantly between AN recipient mice (T1 and T2) and non-AN recipient mice following 4 weeks of colonization. Enteric microbiotas from recipient mice colonized with AN T1 and AN T2 fecal microbiotas were more similar to each other compared with enteric microbiotas from non-AN recipient mice. Specific bacterial families in the Actinobacteria, Bacteroidetes, and Firmicutes phyla were significantly associated with body weight, fat mass, and cecum weight irrespective of the donor group. These data suggest that body weight, fat mass, and cecum weight of colonized GF mice are associated with human fecal microbes and independent of donor AN status, although additional analyses with larger cohorts are warranted.

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales

Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.

Biomarkers of Gut Microbiota in Chronic Spontaneous Urticaria and Symptomatic Dermographism

Background

Chronic urticaria (CU) is a chronic inflammatory skin disease associated with Th2 immune response. The two most common subtypes of CU, i.e., chronic spontaneous urticaria and symptomatic dermographism (CSD), often coexist. However, the pathogenesis of CSD is still unclear. Gut microbiota plays an important role in immune-related inflammatory diseases. The purpose of this study was to explore the correlation between gut microbiota and CSD.

Methods

A case-control study was conducted on CSD patients as well as gender- and age-matched normal controls (NCs). The 16S ribosomal DNA sequencing of fecal samples was used to detect the gut microbiota of all subjects. QPCR was used to further verify the species with differences between the two groups.

Results

The alpha diversity of gut microbiota decreased in CSD patients, accompanied by significant changes of the structure of gut microbiota. Subdoligranulum and Ruminococcus bromii decreased significantly in CSD patients and had a potential diagnostic value for CSD according to receiver operating characteristic curve (ROC) analysis. Enterobacteriaceae and Klebsiella were found to be positively correlated with the duration of CSD, while Clostridium disporicum was positively correlated with the dermatology life quality index (DLQI).

Conclusions

The gut microbiota of CSD patients is imbalanced. Subdoligranulum and Ruminococcus bromii are the gut microbiota biomarkers in CSD.

Methane-dependent selenate reduction by a bacterial consortium

Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.