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Journal of Animal Science Apr 2021Mastitis is an economically important disease and its subclinical state is difficult to diagnose, which makes mitigation more challenging. The objectives of this study...
Mastitis is an economically important disease and its subclinical state is difficult to diagnose, which makes mitigation more challenging. The objectives of this study were to screen clinically healthy ewes in order to 1) identify cultivable microbial species in milk, 2) evaluate somatic cell count (SCC) thresholds associated with intramammary infection, and 3) estimate relationships between udder and teat morphometric traits, SCC, and ewe productivity. Milk was collected from two flocks in early (<5 d) and peak (30 to 45 d) lactation to quantify SCC (n = 530) and numerate cultivable microbial species by culture-based isolation followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; n = 243) identification. Within flock and lactation stage, 11% to 74% (mean = 36%) of samples were culture positive. More than 50 unique identifications were classified by MALDI-TOF MS analysis, and Bacillus licheniformis (18% to 27%), Micrococcus flavus (25%), Bacillus amyloliquefaciens (7% to 18%), and Staphylococcus epidermidis (26%) were among the most common within flock and across lactation stage. Optimum SCC thresholds to identify culture-positive samples ranged from 175 × 103 to 1,675 × 103 cells/mL. Ewe productivity was assessed as total 120-d adjusted litter weight (LW120) and analyzed within flock with breed, parity, year, and the linear covariate of log10 SCC (LSCC) at early or peak lactation. Although dependent on lactation stage and year, each 1-unit increase in LSCC (e.g., an increase in SCC from 100 × 103 to 1,000 × 103 cells/mL) was predicted to decrease LW120 between 9.5 and 16.1 kg when significant. Udder and teat traits included udder circumference, teat length, teat placement, and degree of separation of the udder halves. Correlations between traits were generally low to moderate within and across lactation stage and most were not consistently predictive of ewe LSCC. Overall, the frequencies of bacteria-positive milk samples indicated that subclinical mastitis (SCM) is common in these flocks and can impact ewe productivity. Therefore, future research is warranted to investigate pathways and timing of microbial invasion, genomic regions associated with susceptibility, and husbandry to mitigate the impact of SCM in extensively managed ewes.
Topics: Animals; Cell Count; Female; Lactation; Mammary Glands, Animal; Mastitis; Micrococcus; Milk; Pregnancy; Sheep
PubMed: 33630062
DOI: 10.1093/jas/skab059 -
Annals of Clinical Microbiology and... May 2024Chronic endometritis (CE) is associated with poor reproductive outcomes, yet the role of endometrial microbiota in patients with recurrent implantation failure (RIF) and...
BACKGROUND
Chronic endometritis (CE) is associated with poor reproductive outcomes, yet the role of endometrial microbiota in patients with recurrent implantation failure (RIF) and CE remains unclear. This study aims to characterize endometrial microbiota in RIF patients with CE and assess its implications for reproductive outcomes.
METHODS
In this prospective study, we enrolled RIF patients both with and without CE. Endometrial and cervical samples were collected for 16 S rRNA gene sequencing. Microbiota composition was compared between groups using diversity indices, phylum, and genus-level analysis. Canonical correlation analysis (CCA) and Spearman's correlation coefficients were used to assess relationships between CE, reproductive outcomes, and microbiota. Predictive functional profiling was performed to evaluate metabolic pathways associated with CE.
RESULTS
Endometrial microbiota in CE patients exhibited greater diversity and evenness compared to non-CE patients. Principal coordinates analysis (PCoA) revealed distinct clustering between CE and non-CE groups. Linear discriminant analysis (LDA) identified Proteobacteria, Aminicenantales, and Chloroflexaceae as characteristic of CE, while Lactobacillus, Acinetobacter, Herbaspirillum, Ralstonia, Shewanela, and Micrococcaceae were associated with non-CE. CCA demonstrated associations between CE, adverse reproductive outcomes, and specific bacterial taxa. Microbial metabolic pathways significantly differed between CE and non-CE groups, with enrichment in pathways related to cofactors, vitamins, secondary metabolites, and the immune system in CE patients.
CONCLUSION
RIF patients with CE exhibit distinct endometrial microbiota compositions associated with adverse reproductive outcomes. The increased microbial diversity and altered metabolic pathways in CE suggest a potential correlation with reproductive outcomes, although further studies are necessary to elucidate the causal relationship between microbiota alterations and fertility. Modulating the endometrial microbiome may represent a novel therapeutic strategy to improve IVF outcomes in patients with CE.
Topics: Humans; Female; Endometritis; Microbiota; Endometrium; Adult; Prospective Studies; Embryo Implantation; Bacteria; RNA, Ribosomal, 16S; Pregnancy; Chronic Disease; Infertility, Female
PubMed: 38816832
DOI: 10.1186/s12941-024-00710-6 -
BMC Microbiology Aug 2021In unfavourable environment, such as nutrient limitation, some bacteria encased themselves into a three dimensional polymer matrix called biofilm. The majority of...
BACKGROUND
In unfavourable environment, such as nutrient limitation, some bacteria encased themselves into a three dimensional polymer matrix called biofilm. The majority of microbial infections in human are biofilm related, including chronic lung, wound, and ear infections. The matrix of biofilm which consists of extracellular polymeric substances (EPS) causes bacterial colonization on medical implanted device in patients, such as catheter and lead to patient's death. Biofilm infections are harder to treat due to increasing antibiotic resistance compared to planktonic microbial cells and escalating the antibiotic concentration may result into in vivo toxicity for the patients. Special compounds which are non-microbicidal that could inhibit or destroy biofilm formation are called antibiofilm compounds, for example enzymes, anti-quorum sensing, and anti-adhesins. Arthrobacter sp. CW01 produced antibiofilm compound known as amylase. This time our preliminary study proved that the antibiofilm compound was not only amylase, but also protease. Therefore, this research aimed to optimize the production of antibiofilm agents using amylase and protease inducing media. The five types of production media used in this research were brain heart infusion (BHI) (Oxoid), BHI with starch (BHIS), casein with starch (CS), yeast extract with starch (YS), and casein-yeast extract with starch (CYS). Biofilm eradication and inhibition activities were assayed against Pseudomonas aeruginosa (ATCC 27,853) and Staphylococcus aureus (ATCC 25,923).
RESULTS
The results showed that different production media influenced the antibiofilm activity. Addition of starch, casein and yeast extract increased the production of amylase and protease significantly. Higher amylase activity would gradually increase the antibiofilm activity until it reached the certain optimum point. It was shown that crude extracts which contained amylase only (BHI, BHIS and YS) had the optimum eradication activity against P. aeruginosa and S. aureus biofilm around 60-70 %. Meanwhile, CS and CYS crude extracts which contained both amylase and protease increased the biofilm eradication activity against both pathogens, which were around 70-90 %.
CONCLUSIONS
It was concluded that the combination of amylase and protease was more effective as antibiofilm agents against P. aeruginosa and S. aureus rather than amylase only.
Topics: Amylases; Anti-Bacterial Agents; Arthrobacter; Biofilms; Caseins; Culture Media; Humans; Microbial Sensitivity Tests; Peptide Hydrolases; Pseudomonas aeruginosa; Staphylococcus aureus; Starch; Yeasts
PubMed: 34425755
DOI: 10.1186/s12866-021-02294-z -
World Journal of Gastroenterology Sep 2021() a bacterium that infects approximately half of the world's population, is associated with various gastrointestinal diseases, including peptic ulcers, non-ulcer...
BACKGROUND
() a bacterium that infects approximately half of the world's population, is associated with various gastrointestinal diseases, including peptic ulcers, non-ulcer dyspepsia, gastric adenocarcinoma, and gastric lymphoma. As the burden of antibiotic resistance increases, the need for new adjunct therapies designed to facilitate eradication and reduce negative distal outcomes associated with infection has become more pressing. Characterization of the interactions between , the fecal microbiome, and fecal fatty acid metabolism, as well as the mechanisms underlying these interactions, may offer new therapeutic approaches.
AIM
To characterize the gut microbiome and metabolome in . patients in a socioeconomically challenged and underprivileged inner-city community.
METHODS
Stool samples from 19 patients and 16 control subjects were analyzed. gene sequencing was performed on normalized pooled amplicons using the Illumina MiSeq System using a MiSeq reagent kit v2. Alpha and beta diversity analyses were performed in QIIME 2. Non-targeted fatty acid analysis of the samples was carried out using gas chromatography-mass spectrometry, which measures the total content of 30 fatty acids in stool after conversion into their corresponding fatty acid methyl esters. Multi-dimensional scaling (MDS) was performed on Bray-Curtis distance matrices created from both the metabolomics and microbiome datasets and a Procrustes test was performed on the metabolomics and microbiome MDS coordinates.
RESULTS
Fecal microbiome analysis showed that alpha diversity was lowest in patients over 40 years of age compared to control subjects of similar age group. Beta diversity analysis of the samples revealed significant differences in microbial community structure between patients and control subjects across all ages. Thirty-eight and six taxa had lower and higher relative abundance in patients, respectively. Taxa that were enriched in patients included Gemellaceae, Micrococcaceae, Gemellales and (. Notably, relative abundance of the phylum Verrucomicrobia was decreased in patients compared to control subjects. Procrustes analysis showed a significant relationship between the microbiome and metabolome datasets. Stool samples from patients showed increases in several fatty acids including the polyunsaturated fatty acids (PUFAs) 22:4n6, 22:5n3, 20:3n6 and 22:2n6, while decreases were noted in other fatty acids including the PUFA 18:3n6. The pattern of changes in fatty acid concentration correlated to the Bacteroidetes:Firmicutes ratio determined by gene analysis.
CONCLUSION
This exploratory study demonstrates -associated changes to the fecal microbiome and fecal fatty acid metabolism. Such changes may have implications for improving eradication rates and minimizing associated negative distal outcomes.
Topics: Feces; Gastrointestinal Microbiome; Helicobacter Infections; Helicobacter pylori; Humans; Metabolome; RNA, Ribosomal, 16S; United States
PubMed: 34588753
DOI: 10.3748/wjg.v27.i33.5575 -
Aging Apr 2019Several studies have reported that gut and lung microbiomes are involved in the process of asthma pathogenesis. However, it remains unclear how perinatal or early-life...
Several studies have reported that gut and lung microbiomes are involved in the process of asthma pathogenesis. However, it remains unclear how perinatal or early-life antibiotic intervention affect adult allergic airway inflammation. We assigned C57BL/6 mice randomly to four experimental groups: normal saline control (NS), ovalbumin (OVA), vancomycin pretreated NS (VAN-NS), and vancomycin pretreated OVA (VAN-OVA). The vancomycin groups were orally given the drug from gestational day 14 to 6 week. An OVA-induced asthma model was then established at 6 weeks of age, and airway inflammation was evaluated. In addition, total DNA was extracted from the feces and lung tissue and used for 16S rDNA gene sequencing, to detect the composition of the microbiome. In the VAN-OVA group, airway inflammation and Th2-related cytokines were found to be significantly increased versus the control groups. Gene sequencing showed that vancomycin treatment attenuated the richness and evenness, and altered the composition of the microbiome in the gut and lung. and were potentially correlated to the severity of allergic airway inflammation. Our study suggests that perinatal and early-life vancomycin intervention aggravates allergic inflammation in adulthood, which might be correlated with imbalanced gut and lung microbiome homeostasis.
Topics: Allergens; Animals; Animals, Newborn; Anti-Bacterial Agents; Asthma; Disease Models, Animal; Female; Homeostasis; Inflammation; Lung; Male; Mice; Mice, Inbred C57BL; Microbiota; Ovalbumin; Pregnancy; Prenatal Exposure Delayed Effects; RNA, Ribosomal, 16S; Vancomycin
PubMed: 30981206
DOI: 10.18632/aging.101901 -
Gels (Basel, Switzerland) Apr 2023Olive oil bigels structured with monoglycerides, gelatin, and κ-carrageenan were designed for the partial substitution of pork backfat in fermented sausages. Two...
Olive oil bigels structured with monoglycerides, gelatin, and κ-carrageenan were designed for the partial substitution of pork backfat in fermented sausages. Two different bigels were used: bigel B60 consisted of 60% aqueous and 40% lipid phase; and bigel B80 was formulated with 80% aqueous and 20% lipid phase. Three different pork sausage treatments were manufactured: control with 18% pork backfat; treatment SB60 with 9% pork backfat and 9% bigel B60; and treatment SB80 with 9% pork backfat and 9% bigel B80. Microbiological and physicochemical analyses were carried out for all three treatments on 0, 1, 3, 6, and 16 days after sausage preparation. Bigel substitution did not affect water activity or the populations of lactic acid bacteria, total viable counts, , and during the fermentation and ripening period. Treatments SB60 and SB80 presented higher weight loss during fermentation and higher TBARS values only on day 16 of storage. Consumer sensory evaluation did not identify significant differences among the sausage treatments in color, texture, juiciness, flavor, taste, and overall acceptability. The results show that bigels can be utilized for the formulation of healthier meat products with acceptable microbiological, physicochemical, and organoleptic characteristics.
PubMed: 37102952
DOI: 10.3390/gels9040340 -
Nature Medicine Apr 2020Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune...
Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune system is unknown. Bacteria-like morphology was identified in pockets of human fetal meconium at mid-gestation by scanning electron microscopy (n = 4), and a sparse bacterial signal was detected by 16S rRNA sequencing (n = 40 of 50) compared to environmental controls (n = 87). Eighteen taxa were enriched in fetal meconium, with Micrococcaceae (n = 9) and Lactobacillus (n = 6) the most abundant. Fetal intestines dominated by Micrococcaceae exhibited distinct patterns of T cell composition and epithelial transcription. Fetal Micrococcus luteus, isolated only in the presence of monocytes, grew on placental hormones, remained viable within antigen presenting cells, limited inflammation ex vivo and possessed genomic features linked with survival in the fetus. Thus, viable bacteria are highly limited in the fetal intestine at mid-gestation, although strains with immunomodulatory capacity are detected in subsets of specimens.
Topics: Autopsy; Bacteria; Bacterial Typing Techniques; Female; Fetus; Gastrointestinal Microbiome; Gestational Age; Humans; Infant, Newborn; Intestinal Mucosa; Intestines; Lactobacillus; Meconium; Microbial Viability; Micrococcaceae; Pregnancy; Pregnancy Trimester, Second; RNA, Ribosomal, 16S
PubMed: 32094926
DOI: 10.1038/s41591-020-0761-3 -
Frontiers in Cellular and Infection... 2021Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this...
Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this study was to compare oral microbial signatures and functional profiling between chronic erythematous candidiasis and healthy subjects. Using shotgun metagenomic sequencing, we analyzed the microbiome in 12 chronic erythematous candidiasis, 12 healthy subjects, and 2 chronic erythematous candidiasis cured by antifungal therapy. We found that the salivary microbiota of chronic erythematous candidiasis was significantly different from that of healthy subjects. Among them, and were the most abundant disease-enriched species (Mann-Whitney U-test, < 0.05). In addition, co-occurrence network analysis showed that formed densely connected modules with oral bacterial species and was mainly positive connected to species. Furthermore, we investigated the functional potentials of the microbiome and identified a set of microbial marker genes associated with chronic erythematous candidiasis. Some of these genes enriching in chronic erythematous candidiasis are involved in eukaryotic ribosome, putative glutamine transport system, and cytochrome bc1 complex respiratory unit. Altogether, this study revealed the changes of oral microbial composition, the co-occurrence between and oral bacteria, as well as the changes of microbial marker genes during chronic erythematous candidiasis, which provides evidence of oral microbiome as a target for the treatment and prevention of chronic erythematous candidiasis.
Topics: Candidiasis, Oral; Humans; Metagenomics; Microbiota; Micrococcaceae
PubMed: 34490138
DOI: 10.3389/fcimb.2021.691092 -
BMC Genomics Mar 2017Computational drug design approaches are important for shortening the time and reducing the cost for drug discovery and development. Among these methods, molecular...
BACKGROUND
Computational drug design approaches are important for shortening the time and reducing the cost for drug discovery and development. Among these methods, molecular docking and quantitative structure activity relationship (QSAR) play key roles for lead discovery and optimization. Here, we propose an integrated approach with core strategies to identify the protein-ligand hot spots for QSAR models and lead optimization. These core strategies are: 1) to generate both residue-based and atom-based interactions as the features; 2) to identify compound common and specific skeletons; and 3) to infer consensus features for QSAR models.
RESULTS
We evaluated our methods and new strategies on building QSAR models of human acetylcholinesterase (huAChE). The leave-one-out cross validation values q and r of our huAChE QSAR model are 0.82 and 0.78, respectively. The experimental results show that the selected features (resides/atoms) are important for enzymatic functions and stabling the protein structure by forming key interactions (e.g., stack forces and hydrogen bonds) between huAChE and its inhibitors. Finally, we applied our methods to arthrobacter globiformis histamine oxidase (AGHO) which is correlated to heart failure and diabetic.
CONCLUSIONS
Based on our AGHO QSAR model, we identified a new substrate verified by bioassay experiments for AGHO. These results show that our methods and new strategies can yield stable and high accuracy QSAR models. We believe that our methods and strategies are useful for discovering new leads and guiding lead optimization in drug discovery.
Topics: Acetylcholinesterase; Amino Acids; Arthrobacter; Bacterial Proteins; Drug Design; Enzyme Inhibitors; GPI-Linked Proteins; Histamine; Humans; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Ligands; Molecular Docking Simulation; Oxidoreductases; Quantitative Structure-Activity Relationship; Static Electricity; Substrate Specificity
PubMed: 28361681
DOI: 10.1186/s12864-017-3503-2 -
Journal of Clinical Microbiology Apr 2023Rothia, Kocuria, Arthrobacter, and Pseudoglutamicibacter are bacterial species within the family . Knowledge of human infections due to these bacteria is limited. This... (Observational Study)
Observational Study
Rothia, Kocuria, Arthrobacter, and Pseudoglutamicibacter are bacterial species within the family . Knowledge of human infections due to these bacteria is limited. This study aimed to examine features of infections caused by non-Micrococcus (NMM). Findings of NMM from blood cultures and other sterile cultures from 2012 to 2021 were identified from the records of the Department of Clinical Microbiology in Region Skåne, Lund, Sweden. Medical records were retrospectively reviewed. True infection was defined as having signs of infection, no other more likely pathogen, and no other focal infection, together with two positive blood cultures or one positive blood culture and an intravascular device. A total of 197 patients with findings of NMM in blood cultures were included. Among adult patients with bacteremia, 29 patients (22%) were considered to have a true infection. Adults with true infection were significantly more likely to have malignancy (69%), leukopenia (62%), and treatment with chemotherapeutics (66%) compared to patients with contaminated samples (24%, 3%, and 8%, respectively) (0.001). A total of 31 patients had findings of NMM in other sterile cultures, and infections were considered true in joints (= 4), a pacemaker (= 1), and peritoneal dialysis fluid (= 1). Infections due to NMM occur but are rare. Growth of NMM in blood cultures should be suspected to be a true infection mainly in immunocompromised patients.
Topics: Adult; Humans; Micrococcaceae; Micrococcus; Arthrobacter; Retrospective Studies; Bacteremia
PubMed: 36946723
DOI: 10.1128/jcm.01484-22