16S RNA Research Articles

RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.

RNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search algorithm that finds and ranks independent RNA substructures. Our expanded list of 183 existing dual graph motifs reveals five common motifs found in transfer RNA, riboswitch, and ribosomal 5S RNA components. Moreover, we identify three motifs for available viral frameshifting RNA elements, suggesting a correlation between viral structural complexity and frameshifting efficiency. We further partition the RNA substructures into 1844 distinct submotifs, with pseudoknots and junctions retained intact. Common modules are internal loops and three-way junctions, and three submotifs are associated with riboswitches that bind nucleotides, ions, and signaling molecules. Together, our library of existing RNA motifs and submotifs adds to the growing universe of RNA modules, and provides a resource of structures and substructures for novel RNA design.

Distinct alterations of fecal microbiota refer to the efficacy of adalimumab in Crohn's disease.

Background and Aims: Anti-tumor necrosis factor mAb (i.e., adalimumab, ADA) is currently used in the treatment of patients with Crohn’s disease (CD). However, its regulation on fecal microbiota is still not fully understood. Methods: A retrospective analysis was conducted on 115 patients with CD who received treatment with ADA for 12 weeks at the Inflammatory Bowel Disease Center in Shanghai Tenth People’s Hospital and Department of Gastroenterology in Shanghai General Hospital. The Crohn’s disease activity index (CDAI) evaluation was applied to patients before ADA therapy at week 0, 4, 8, and 12. Clinical remission (CR) was defined as the CDAI < 150. All patients underwent ileocolonoscopy or enteroscopy at baseline (week 0) and week 12. Crohn’s Disease Endoscopic Index of Severity (CDEIS) scores were calculated by two experienced physicians to assess endoscopic activity. Mucosal healing (MH) was assigned a CDEIS score between 0 and 3. Fecal samples were collected from eight CD patients at baseline and week 12, and the microbiota was analyzed by using 16S RNA sequencing. Results: At week 12, CR was achieved in 70.6% (72/102) of the patients with active CD. A total of 47.1% (48/102) of the patients with active CD attained MH, among which, 56.6% (30/53) of the patients with mildly active CD (3 ≤ CDEIS <9) and 48.0% (12/25) of the moderately active CD patients (9 ≤ CDEIS <12) attained MH, but only 25.0% (6/24) achieved MH in severely active CD patients (CDEIS ≥12). The efficacy of ADA was not associated with lesion locations (χ 2 = 0.409, p = 0.815). Unexpectedly, we found an increase in protective microbiota at the genus level (e.g., Barnesiella, Anaerostipes, Tyzzerella, Lachnoclostridium, and Lachnospiraceae_unclassified) but a decrease in pathogenic bacteria (Escherichia–Shigella) in fecal samples of the ADA-responsive group (ADA-R) when compared with those in the ADA-nonresponsive group (ADA-NR). Notably, the gene bglX coding β-glucosidase and gph encoding phosphoglycolate phosphatase were enriched in fecal samples of ADA-R. Conversely, the abundance of genes coding ATP-binding cassette (ABC) transporter system proteins was significantly enriched in fecal samples of ADA-NR when compared with that of the ADA-R. Conclusion: This study reveals that ADA markedly improves clinical remission and induces MH in mildly to moderately active CD patients and that distinct changes in the gut microbiota can be used to predict the efficacy of ADA.

Postnatal growth and gut microbiota development influenced early childhood growth in preterm infants.

BackgroundPreterm infants are at high risk for growth failure and childhood weight problems due to the disruption of normal intrauterine growth and nutrition. Early nutritional support and microbiome acquisition can play an important role in childhood growth.ObjectiveOur study examined potential postnatal indicators, including gut bacterial compositions, macronutrients, and catch-up growth, of growth pattern from infancy into early childhood.MethodsThis is a retrospective study of preterm infants born < 35 weeks who were followed up in the university complex care clinic from 2012–2018. Weight and length z-scores at birth, 1, 2, 4, 6, 12 and 15 months, and body mass index (BMI) and length z-scores from 2 to 5 years of age were collected. Catch-up growths were calculated by changes in z-scores and divided into early (birth-4 months) and late (4–18 months). Postnatal nutritional data and fecal samples were collected. Fecal microbiome data obtained from 16S RNA V4 sequencing was analyzed against clinical and growth data using a regression model.Results160 infants included in the final analysis had birth weight and gestational age of 1,149 ± 496 grams and 28 ± 3 weeks. Early weight gain positively correlated with length z-scores but not with BMI at 2 years of age. BMI at 2 years of age strongly correlated with BMI at 3, 4, and 5 years of age. Postnatal abundance of Gammaproteobacteria was negatively associated with early growth while Bacteroides and Lactobacillus were positively associated with childhood BMI.ConclusionOur findings suggest that optimal postnatal nutrition promoted early catch-up growth in weight as well as improved linear growth without influence on childhood BMI. Postnatal gut microbial colonization, which is a modifiable factor, was associated with childhood growth in preterm infants.

Evaluation of the Efficacy of Enterococcus faecium L3 as a Feed Probiotic Additive in Chicken.

The study was devoted to the comparison of the probiotic effect of enterococcal Enterococcus faecium L3 to the antibiotic enramycin as a chicken feed additive. Two hundred and sixteen chickens were divided into three groups and tested by different parameters including weight gain, food consumption, blood biochemistry, immunology, and caecal microbiome at two checkpoints, 21 and 39days after birth. By the end of the experiment, a group of chickens getting probiotic demonstrated weight gain of more than 100g at the average relative to the control group with no additive in animal feed (P < 0.05). Blood serum biochemistry showed a significant increase in HDL level (P < 0.05) relative to the control group. The 16S RNA sequencing demonstrated the growth abundance of Lachnospiraceae and the decrease of Proteobacteria in probiotic fed group. On the contrary, the antibiotic fed group showed a noticeable increase in the abundance of Proteobacteria which included the genus Salmonella. Thus, probiotic E. faecium L3 being added to chicken food as a single additive may be considered as a possible replacement of antibiotic enramycin.

Exploring the Correlation between Changes in Gut Microbial Community Diversity and Depression in Human Populations.

Depression, also known as depressive disorder, is a group of psychosomatic affective disorders characterized by persistent and significantly depressed mood, delayed thinking, and cognitive impairment. The aim of this study was to explore the correlation between changes in gut microbial community diversity and depression to provide data on new strategies for the prevention and treatment of depression. In this study, we separated participants into a group of depressed patients and a healthy comparison group. We analyzed the gut microbial community structure of depressed patients and healthy comparisons using second-generation sequencing of the bacterial 16S RNA gene. There were significant differences in the gut microflora structure between patients with depression and healthy individuals. The gut flora alpha diversity index was significantly reduced in patients with depression compared to that in the healthy population. At the species level, the relative abundance of Coprococcus catus and Bacteroides barnesiae was significantly lower in the depressed group than that in the control group. The development of depression may be associated with a decrease in beneficial gut bacteria.

Cervicovaginal Complement Activation and Microbiota During Pregnancy and in Parturition.

BackgroundVaginal microbiome and the local innate immune defense, including the complement system, contribute to anti- and proinflammatory homeostasis during pregnancy and parturition. The relationship between commensal vaginal bacteria and complement activation during pregnancy and delivery is not known.ObjectiveTo study the association of the cervicovaginal microbiota composition to activation and regulation of the complement system during pregnancy and labor.Study designWe recruited women during late pregnancy (weeks 41 + 5 to 42 + 0, n=48) and women in active labor (weeks 38 + 4 to 42 + 2, n=25). Mucosal swabs were taken from the external cervix and lateral fornix of the vagina. From the same sampling site, microbiota was analyzed with 16S RNA gene amplicon sequencing. A Western blot technique was used to detect complement C3, C4 and factor B activation and presence of complement inhibitors. For semiquantitative analysis, the bands of the electrophoresed proteins in gels were digitized on a flatbed photo scanner and staining intensities were analyzed using ImageJ/Fiji win-64 software. Patient data was collected from medical records and questionnaires.ResultsThe vaginal microbiota was Lactobacillus-dominant in most of the samples (n=60), L. iners and L. crispatus being the dominant species. L. gasseri and L. jensenii were found to be more abundant during pregnancy than active labor. L. jensenii abundance correlated with C4 activation during pregnancy but not in labor. Gardnerella vaginalis was associated with C4 activation both during pregnancy and labor. The amount of L. gasseri correlated with factor B activation during pregnancy but not during labor. Atopobium vaginae was more abundant during pregnancy than labor and correlated with C4 activation during labor and with factor B activation during pregnancy. Activation of the alternative pathway factor B was significantly stronger during pregnancy compared to labor. During labor complement activation may be inhibited by the abundant presence of factor H and FHL1.ConclusionsThese results indicate that bacterial composition of the vaginal microbiota could have a role in the local activation and regulation of complement-mediated inflammation during pregnancy. At the time of parturition complement activation appears to be more strictly regulated than during pregnancy.

Oral microbiota signatures in post-traumatic stress disorder (PTSD) veterans.

Post-traumatic stress disorder (PTSD) represents a global public health concern, affecting about 1 in 20 individuals. The symptoms of PTSD include intrusiveness (involuntary nightmares or flashbacks), avoidance of traumatic memories, negative alterations in cognition and mood (such as negative beliefs about oneself or social detachment), increased arousal and reactivity with irritable reckless behavior, concentration problems, and sleep disturbances. PTSD is also highly comorbid with anxiety, depression, and substance abuse. To advance the field from subjective, self-reported psychological measurements to objective molecular biomarkers while considering environmental influences, we examined a unique cohort of Israeli veterans who participated in the 1982 Lebanon war. Non-invasive oral 16S RNA sequencing was correlated with psychological phenotyping. Thus, a microbiota signature (i.e., decreased levels of the bacteria sp_HMT_914, 332 and 871 and Noxia) was correlated with PTSD severity, as exemplified by intrusiveness, arousal, and reactivity, as well as additional psychopathological symptoms, including anxiety, hostility, memory difficulties, and idiopathic pain. In contrast, education duration correlated with significantly increased levels of sp_HMT_871 and decreased levels of Bacteroidetes and Firmicutes, and presented an inverted correlation with adverse psychopathological measures. Air pollution was positively correlated with PTSD symptoms, psychopathological symptoms, and microbiota composition. Arousal and reactivity symptoms were correlated with reductions in transaldolase, an enzyme controlling a major cellular energy pathway, that potentially accelerates aging. In conclusion, the newly discovered bacterial signature, whether an outcome or a consequence of PTSD, could allow for objective soldier deployment and stratification according to decreases in sp_HMT_914, 332, 871, and Noxia levels, coupled with increases in Bacteroidetes levels. These findings also raise the possibility of microbiota pathway-related non-intrusive treatments for PTSD.

Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.

Bifidobacterium longum BL-10 with Antioxidant Capacity Ameliorates Lipopolysaccharide-Induced Acute Liver Injury in Mice by the Nuclear Factor-κB Pathway.

Bifidobacterium longum is frequently utilized and has broad prospects for preventing liver injury. The current research assessed the antioxidant capacity of B. longum BL-10 and probed its mechanism for ameliorating lipopolysaccharide (LPS)-induced acute liver injury (ALI). B. longum BL-10-encoded 15 antioxidant genes showed strong reducing power activity and scavenging activity of DPPH, hydroxyl radicals, and superoxide anions. The intragastric administration of B. longum BL-10 resulting in a marked reduction in liver function indicators (alanine aminotransferase, aspartate aminotransferase, total bilirubin, and total bile acid) and proinflammatory cytokines (TNF-α, IFN-γ, and IL-6) was indicative of ALI recovery. Following 16s RNA analysis, B. longum BL-10 significantly altered the richness of genera, as for the Escherichia-Shigella, Lachnospiraceae_NK4A136_group, and Clostridia_UCG-014, dramatically contributing to the formation of acetic acid and butyric acid. Meanwhile, their metabolites regulated the TLR4/NF-κB signaling pathways to alleviate hepatic injury symptoms. Overall, all the results demonstrated that B. longum BL-10 had excellent efficiency in preventing LPS-induced ALI.

Alteration of microbiota antibody‐mediated immune selection contributes to dysbiosis in inflammatory bowel diseases

Human secretory immunoglobulins (SIg) A1 and SIgA2 guide mucosal responses toward tolerance or inflammation, notably through reverse‐transcytosis, the apical‐to‐basal transport of IgA2 immune complexes via M cells of gut Peyer's patches. As such, the maintenance of a diverse gut microbiota requires broad affinity IgA and glycan–glycan interaction. Here, we asked whether IgA1 and IgA2‐microbiota interactions might be involved in dysbiosis induction during inflammatory bowel diseases. Using stool HPLC‐purified IgA, we show that reverse‐transcytosis is abrogated in ulcerative colitis (UC) while it is extended to IgA1 in Crohn's disease (CD). 16S RNA sequencing of IgA‐bound microbiota in CD and UC showed distinct IgA1‐ and IgA2‐associated microbiota; the IgA1+ fraction of CD microbiota was notably enriched in beneficial commensals. These features were associated with increased IgA anti‐glycan reactivity in CD and an opposite loss of reactivity in UC. Our results highlight previously unknown pathogenic properties of IgA in IBD that could support dysbiosis.

Бактериялық обырдың таза штамын алып ағаш тектестерге инфекциялық белсенділігін in vitro жағдайында зерттеу

Dense and diverse primary forests, which nourish the soil, emit a large amount of oxygen, are the dream of every state. Therefore, the first President of Kazakhstan N. Nazarbayev ordered to make a large green zone around Nur-Sultan, which is being improved and refined every year. This project is designed to turn the capital of Kazakhstan, the city of Nur-Sultan, into a green belt, completely sowing forests around the city, the area of which is 100 thousand hectares. Properly grafted woody plants in the green belt, in addition to enriching the air with oxygen, decorating landscapes, should contribute to the ventilation of zones, the removal of polluted air from residential and industrial zones, the formation of vertical air flows and the dispersion of polluted air in higher layers of the atmosphere, as well as air purification from various aerosols, dust, soot, and heat. Nevertheless, all these natural resources are under great threat due to the prevalence of a little-studied disease-bacterial cancer of tree species. Currently, such a disease is observed in ashkortostan, the Baltic States, Tatarstan, the Republic of Adygea, the European part of Russia, as well as in Bryansk and adjacent regions. In these countries, the coverage of tree species with this disease is increasing, which creates a real threat of the tree trunks drying. Bacterial cancer of tree species is also found in Kazakhstan. In this regard, the study of this disease is relevant, since due to the characteristics of the lesion of trees, the diagnosis of the disease, forest-taxational and landscape conditions, its spread has not been fully studied. The purpose of our work is to take core samples from birch (Betula rendula Roth.), which grows in the forests of the Green Belt surrounded by the city of Nur-Sultan, with signs of bacterial cancer (dropsy); obtain core samples from the trunk, to cultivate isolated bacterial cultures on nutrient media; to obtain pure strains of the causative agent of the disease, molecular identification of the nucleotide chain of ribosomal RNA 16S. In addition, the determination of the molecular characteristics of the obtained bacterial strains in accordance with the typical type of Dickeya dadantii on the international basis of Gene Bank. In the course of the study, the infectious activity of this strain of bacteria on other woody analogues was studied in vitro. Inoculation of birch leaves and catkins that have not undergone bacterial cancer with Dickeya dadantii strains isolated by us in vitro showed complete virulence of the pathogen to the experimental birch population, i.e. infectious activity.

P-097 The Microbiota Difference in Normal and Abnormal Semen Samples Assessed by Real-time RCR

Abstract Study question Does microbiota differ in semen samples with normal and abnormal parameters? Summary answer The higher prevalence of obligate anaerobes and lactobacilli was more typical for semen samples with abnormal parameters compared to samples with normozoospermia. What is known already For a long time, semen in healthy men was considered to be sterile, and the detection of microorganisms was associated with pathologies. More recently, it has been shown that microbiota can be present in semen samples with normal semen parameters. Some researchers, usually using 16S RNA sequencing, cautiously suggested that certain microbial groups could be associated with norm and pathology. Study design, size, duration 825 semen samples from men who came to the “Garmonia” Medical Center (Yekaterinburg, Russia) seeking preconception care in 2019-2021, were included in the study. Depending on the spermiograms results, the samples were divided into two groups: Group 1 – normozoospermia (n = 350), Group 2 – samples with abnormal parameters (n = 475). Participants/materials, setting, methods Semen microbiota was analyzed by real-time PCR Androflor kit (DNA Technology, Russia). Detection rates of 18 bacteria/bacterial groups and 4 consolidated groups of microorganisms (obligate anaerobes (OA), gram-positive facultative anaerobes (GPFA), gram-negative facultative anaerobes GNFA), and mycoplasmas) were compared in Group 1 and Group 2. Two-tailed Fisher’s exact test was performed to check the significance of the differences. Main results and the role of chance Bacterial DNA was detected more often in the samples with abnormal spermiograms (Group 2) than in normozoospermia samples (Group 1): 79.6% and 73.4% respectively (p = 0.045). There was no difference in detection rates of GPFA, GNFA and mycoplasmas in both groups, whereas the detection rate of OA was significantly higher in Group 2 samples than in Group 1 (44.0% and 36.3%, respectively, p = 0.026). When analyzing the detection rate of different bacteria/bacterial groups we registered significant differences for 7 of them. For all the groups, the higher detection rate was associated with Group 2 (abnormal semen samples). In these samples, the detection rate of lactobacilli was 23.4% (compared to 13.7% in Group 1, p &amp;lt; 0.001), Megasphaera spp./Veillonella spp./Dialister spp. – 21.1 (12.0% in Group 1, p = 0.001), Bacteroides spp./Porphyromonas spp./Prevotella spp. – 26.7% (17.1% in Group 1, p = 0.001), Anaerococcus spp. – 15.2% (9.7% in Group 1, p = 0.021), Peptostreptococcus spp./Parvimonas spp. – 18.1% (12.3% in Group 1, p = 0.026), Eubacterium spp. – 24.8% (18.9% in Group 1, p = 0.043). Limitations, reasons for caution Androflor PCR kit uses the 103 genome-equivalent/ml threshold for most of the target microbial groups; samples with lower DNA level are considered as negative. Hence, it is possible that the results may be different when using another threshold. Wider implications of the findings Further research should determine the microbiota variants in semen samples with different abnormalities, such as asthenozoospermia, leukospermia, etc. These findings could expand our understanding of the contribution made by specific microorganisms to diseases, which potentially could lead to the development of new therapeutic options or improvement of the existing ones. Trial registration number Ethics Committee of Ural State Medical University (Protocol № 7 dated September 20, 2019)

Inhibitory relationships of resident bacteria isolated from the mantle fluids of Crassostrea virginica.

Thirteen aerobic, halotolerant marine bacterial strains were isolated from the mantle fluids and associated mucus of the eastern oyster Crassostrea virginica harvested from the highly impacted Black Rock Harbor in western Long Island Sound. All isolated strains were Gram negative and had previously been identified using 16S RNA gene sequence analysis. These 13 strains were examined for their ability to inhibit the growth of each other employing a diffusion agar method used by antibiotic assays. All challenger strains were able to inhibit at least one of the indicator isolates. Enhanced antimicrobial activity was observed from cultures of Pseudoalteromonas sp. (L), Shewanella sp. (H), Thalassospira sp. (JA), and Alteromonas sp. (JB) when used to challenge the indicator isolates. The indicator isolate most sensitive to antimicrobial activity was another Pseudoalteromonas species (KC) whose growth was inhibited by 10 of the challenger strains, whereas Pseudoalteromonas (L) was resistant to all growth challenges. Growth autoinhibition was observed with isolates Tenacibaculum ascidiaceicola (KC), Vibrio (B), and Shewanella (H) during a 24 h incubation. No antimicrobial growth inhibition was detected when 24 and 48 h cell-free extracts of these isolates were used to challenge indicator isolate growth.

Characterization of the pathogenicity of a Bacillus cereus isolate from the Mariana Trench

ABSTRACT Bacillus cereus is an important opportunistic pathogen widely distributed in the environment. In this study, we reported the isolation and characterization of a B. cereus isolate, MB1, from the Challenger Deep of the Mariana Trench. MB1 is aerobic, motile, and able to form endospores. It possesses 5966 genes distributed on a circular chromosome and two plasmids. The MB1 genome contains 14 sets of 23S, 5S, and 16S ribosomal RNA operons, 106 tRNA genes, 4 sRNA genes, 12 genomic islands, 13 prophages, and 302 putative virulence genes, including enterotoxins and cytolysins. Infection studies showed that MB1 was able to cause acute and lethal infection in fish and mice, and was highly toxic to mammalian cells. MB1 induced, in a dose-dependent manner, pyroptotic cell death, characterized by activation of caspase-1, cleavage of gasdermin D, and release of IL-1β and IL-18. MB1 spores exhibited swimming and haemolytic capacity, but were severely attenuated in pathogenicity, which, however, was regained to the full extent when the spores germinated under suitable conditions. Taken together, these results provide new insights into the biological and pathogenic mechanism of deep sea B. cereus.

7S RNA is surveilling mitochondrial DNA transcription

7S RNA is surveilling mitochondrial DNA transcription

Examination of host genetic effects on nasal microbiome composition

Genetic predisposition increases risk for asthma, and distinct nasal microbial compositions are associated with asthma. Host genetics might shape nasal microbiome composition. We examined associations between host genetics and nasal microbiome composition. Nasal samples were collected from 584 participants from the Mount Sinai Health System, New York. Seventy-seven follow-up samples were collected from a subset of 40 participants. 16S rRNA sequencing and RNA sequencing were performed on nasal samples. Beta diversity was calculated, variant calling on RNA sequencing data was performed, and genetic relatedness between individuals was determined. Using linear regression models, we tested for associations between genetic relatedness and nasal microbiome composition. The median age of the cohort was 14.6 (interquartile range 11.2-19.5) years, with participants representing diverse ancestries and 52.7% of the cohort being female. For participants who provided follow-up samples, the median time between samples was 5.1 (interquartile range 1.4-7.2) months. Nasal microbiome composition similarity as reflected by beta diversity was significantly higher within subjects over time versus between subjects (coefficient= 0.091, P= 2.84-7). There was no significant association between genetic relatedness and beta diversity (coefficient= -0.05, P= .29). Additional analyses exploring the relationship between beta diversity and genetic variance yielded similar results. Host genetics has little influence on nasal microbiome composition.

Abstract 3061: Elevated bile acid metabolism is associated with breast cancer microbiome, less cell proliferation, and better survival

Abstract BACKGROUND: Bile acids are generated and secreted by hepatocytes and are involved in intestinal circulation. Recently it has been reported that specific bile acids are accumulated in the breast cancer tumor microenvironment (TME), leading to a favorable prognosis for patients and reducing the aggressiveness and metastatic potential of the cancer. We hypothesized that breast cancers with increased bile acid metabolism may have a favorable clinical outcome due to the suppression of cancer cell proliferation. MATERIALS AND METHODS: We analyzed total of 6285 patients from three independent breast cancer cohorts with TCGA as an exploring cohort and METABRIC, GSE96058 as validation cohorts. We divided each cohort into "high" and "low" groups by the top and bottom quartiles of the score following the previous reports. RESULTS: High bile acid metabolism breast cancer enriched multiple metabolic pathway gene sets such as fatty acid and xenobiotic metabolism, as well as adipogenesis and protein secretion by gene set enrichment analysis (GSEA). Adipocytes and preadipocytes were significantly infiltrated in the high score group. Considering the possibility that activation of bile acid metabolism is due to accumulation of microbiome-derived bile acids in breast cancer, we identified that four microorganisms (Anaerococcus, Collimonas, Gammaretrovirus and Hymenobacter) significantly correlated with the bile acid metabolism using TCGA 16s RNA seq data. Surprisingly, protein secretion gene set was significantly enriched to tumors that are abundant in three out of four of these bacterial species. This may suggest that bile acid metabolism are elevated in response to bile acids secreted by the microbiome present in breast cancer TME. The bile acid metabolism was highest in ER+HER2- and lowest in triple-negative, the most aggressive form of breast cancer. The score was negatively correlated with Ki67 gene expression and histological grade, consistent with previous reports that breast cancers with high bile acid accumulation were less proliferative. In agreement, breast cancers with low bile acid metabolism was associated with significantly high silent and non-silent mutation rates, Intratumor Heterogeneity, Proliferation score and Homologous Recombination Defects, and enriched G2M checkpoint gene set. Finally, survival analysis showed that high bile acid metabolism group had significantly better disease free, disease specific and overall survival. CONCULUSIONS: Bile acid metabolism was associated with involvement of microbiome in TME, the suppression of cell proliferation, and better prognosis in breast cancer. Citation Format: Rongrong Wu, Quratulain Sabih, Masanori Oshi, Takashi Ishikawa, Li Yan, Kazuaki Takabe. Elevated bile acid metabolism is associated with breast cancer microbiome, less cell proliferation, and better survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3061.

Hydrocarbons removal from real marine sediments: Analysis of degradation pathways and microbial community development during bioslurry treatment

In this study, real marine sediments polluted by petroleum compounds were treated by means of a bioslurry pilot scale reactor. The treatment performance was evaluated by measuring the removal of total petroleum hydrocarbon (TPH), coupled to further analyses required to understand the mechanisms involved in the biodegradation process. The maximum TPH-removal efficiency reached 86 % at the end of experiments. Moreover, high throughput 16S RNA gene sequencing was used to describe the microbiome composition in sediment prior to, and after, bioslurry treatment, in order to identify the taxa mostly entailed in the TPH removal process. The raw sediment was mostly colonized by members of Sulfurimonas genus; after bioslurry treatment, it was noticed a shift in the microbial community composition, with Proteobacteria phylum dominating the remediation environment (high increase in terms of growth for Hydrogenophaga and Sphingorhabdus genera) along with the Phaeodactylibacter genus (Bacteroidetes). Furthermore, the assessment of gaseous emissions from the system allowed to quantify the volatile hydrocarbon component and, consequently, to obtain a more accurate evaluation of TPH-removal pathway by the bioslurry system. Finally, phytotoxicity tests on sediment samples highlighted an increase of the treated sample quality status compared to the untreated one.

Bacterial vaginosis pattern and antibiotic susceptibility testing in female patients using high vaginal swabs

Abstract. Al-Kraety IAA, Al-Muhanna SG, Banoon SR, Ghasemian A. 2022. Bacterial vaginosis pattern and antibiotic susceptibility testing in female patients using high vaginal swabs. Biodiversitas 23: 2838-2844. Bacterial species found in the vaginal environment encompass a wide variety of species. A common cause of vaginal discharge in women is bacterial vaginosis BV (BV). Various Gram-positive and Gram-negative rod shaped bacteria, including E. coli, Klebsiella spp., Enterococcus spp., Enterobacter spp., Raoultella ornithinolytica, and Staphylococcus spp. contribute significantly to bacterial vaginosis. In this study, vaginal swabs (VS) were obtained from 50 individuals with symptoms of vaginal discharge. The swabs were inoculated on blood, Mannitol, and MacConkey agar culture media. Biochemical tests were performed after an overnight incubation period to determine growth and colonial morphology. In addition to VITEK® 2 compact system and PCR technique by using a 16s RNA gene where all bacteria isolates were positive for this gene. Antibiotic sensitivity was investigated through compact VITEK® 2 and sensitivity cards (AST-P580), (AST-N222), and (AST-GN76). The bacterial isolates including 20 (43.4%) of E. coli, 8 (17.3%) of Klebsiella spp. and 8 (17.3%) of Staphylococcus spp. were investigated in present study. Additionally, 4 (8.6%) isolates of Enterobacter spp., 3 (6.5%) of E. faecalis, and 3 (6.5%) of R. ornithinolytica. The E. coli, Staphylococcus spp., Enterobacter spp., E. faecalis and R. ornithinolytica isolates were found resistant to several antibiotics and considered multi-resistance (MDR).

Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Obtained from Wound Infection

Purpose: Wounds infection is frequent hospital acquired infections which is caused by a wide variety of microorganism. Inappropriate treatment could be more hazardous to suffering patients and could lead to death. This manuscript is aimed to identify the existence of Pseudomonas aeruginosa from the clinical samples and determine the molecular evolution and population structure of Pseudomonas species using bioinformatics tools Method: The specimens were swiped from the bandage of infected patients, who were admitted for the therapeutic intervention in the hospitals, localized in Delhi-NCR region. Primarly, specimens were cultured in cetrimide broth for specific growth of Pseudomonas sp. Single colony isolation on cetrimide agar plate and characterization of bacterial colony by producing fluorescence under UV light was done to confirm Pseudomonas aeruginosa (P. aeruginosa). Furthermore, phylogenetic analysis was performed on the basis of PCR and sequencing of 16s rRNA sequence of P. aeruginosa. Results: Assay based on bacterial culture, biochemical and 16S rRNA gene analysis methods confirm the presence of P. aeruginosa in collected wound specimen. Basic local alignment search tool analysis indicates that newly sequenced 16S rRNA gene sequence was shown 99% similarity to P. aeruginosa species, analyzed using NCBI-BLAST tool. The phylogenetic analysis and nucleotide base composition studies performed using 45 sequences of 16S rRNA gene from 18 different species of Pseudomonas, including P. aeruginosa. The phylogenetic analysis was performed using Maximum Likelihood method for evolutionary relationships. Conclusion: The biochemical and molecular characterization revealed that the clinical samples were infected with P. aeruginosa. Further, phylogenetic analysis of 16S RNA sequences revealed evolutionary conservation among different Pseudomonas species.