16S RNA Research Articles

Antibacterial and antioxidant activities of streptomyces sp. Strain FR7 isolated from forest soil.

Actinomycetes produce secondary metabolites with many bioactivities such as antimicrobial, which can be useful as alternatives against resistant bacterial strains. Therefore, the screening of new habitats is likely to provide new strains with high potential. In this work, the antimicrobial capacity was used to select Streptomyces sp. strains isolated from Raf Raf forest (Tunisia). From the strain displaying higher activity, FR7, an ethyl acetate extract was prepared under optimized culturing conditions (10 days at 30 ºC in ISP2 medium with initial pH 8), showing significant antimicrobial activity against Micrococcus luteus and Staphylococcus aureus (MIC=5μg ml-1), and Listeria monocytogenes and Pseudomonas aeruginosa (MIC=20μg ml-1). The extract displayed strong DPPH radical scavenging activity (IC50=1.3µg ml-1) and protection of yeast cells from H2O2-induced oxidative stress determined by flow cytometry with dichlorofluorescein diacetate. The crude extract showed the presence of polyketides, with methylsalicylic acid as moiety, a large and diverse group of secondary metabolites with a wide range of bioactivities, including antioxidant and antibacterial. Based on 16S RNA gene sequences, strain FR7 was identified as belonging to genus Streptomyces with high resemblance to Streptomyces iakyrus. Streptomyces sp. FR7 has great potential as a source of antibacterial and antioxidant metabolites.

The gut microbiota metabolite capsiate regulate SLC2A1 expression by targeting HIF-1α to inhibit knee osteoarthritis-induced ferroptosis.

Ferroptosis is an iron-dependent cell death that has been found to aggravate the progression of osteoarthritis (OA) and gut microbiota- OA axis refers to the bidirectional information network between the gut microbiota and OA, which may provide a new way to protect the OA. However, the role of gut microbiota-derived metabolites in ferroptosis-relative osteoarthritis remains unclear. The objective of this study was to analyze the protective effect of gut microbiota and its metabolite capsiate (CAT) on ferroptosis-relative osteoarthritis in vivo and in vitro experiments. From June 2021 to February 2022, 78 patients were evaluated retrospectively and divided into two groups: The health group (n=39) and the OA group (n=40). Iron and oxidative stress indicators were determined in peripheral blood samples. And then in vivo and in vitro experiments, a surgically destabilized medial meniscus (DMM) mice model was established and treated with CAT or Ferric Inhibitor-1 (Fer-1). Solute Carrier Family 2 Member 1 (SLC2A1) short hairpin RNA (shRNA) was utilized to inhibit SLC2A1 expression. Serum iron was increased significantly but total iron binding capacity was decreased significantly in OA patients than healthy people (p < 0.0001). The least absolute shrinkage and selection operator clinical prediction model suggested that serum iron, total iron binding capacity, transferrin, and superoxide dismutase were all independent predictors of OA (p < 0.001). Bioinformatics results suggested that SLC2A1, Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1), and HIF-1α (Hypoxia Inducible Factor 1 Alpha)-related oxidative stress signaling pathways play an important role in iron homeostasis and OA. In addition, gut microbiota 16s RNA sequencing and untargeted metabolomics were used to find that gut microbiota metabolites CAT in mice with osteoarthritis were negatively correlated with Osteoarthritis Research Society International (OARSI) scores for chondrogenic degeneration (p=0.0017). Moreover, CAT reduced ferroptosis-dependent osteoarthritis in vivo and in vitro. However, the protective effect of CAT against ferroptosis-dependent osteoarthritis could be eliminated by silencing SLC2A1. SLC2A1 was upregulated but reduced the SLC2A1 and HIF-1α levels in the DMM group. HIF-1α, MALAT1, and apoptosis levels were increased after SLC2A1 knockout in chondrocyte cells (p=0.0017). Finally, downregulation of SLC2A1 expression by Adeno-associated Virus (AAV) -SLC2A1 shRNA improves osteoarthritis in vivo. Our findings indicated that CAT inhibited HIF-1a expression and reduced ferroptosis-relative osteoarthritis progression by activating SLC2A1.

Mitochondrial DNA Polymorphism in HV1 and HV2 Regions and 12S rDNA in Perimenopausal Hypertensive Women.

Estrogens enhance cellular mitochondrial activity. The diminution of female hormones during menopause may have an effect on the mitochondrial genome and the expression of mitochondrial proteins. Hence, oxidative stress and the pro-inflammatory state contribute to the formation of systemic illnesses including arterial hypertension (AH). This study aimed to determine the types and frequency of mutations in the mitochondrial DNA (mtDNA) nucleotide sequence in the hypervariable regions 1 and 2 (HV1 and HV2) and the 12S RNA coding sequence of the D-loop in postmenopausal women with hypertension. In our study, 100 women were investigated, 53 of whom were postmenopausal and 47 of whom were premenopausal (53.9 ± 3.7 years vs. 47.7 ± 4.2 years, respectively). Of those studied, 35 premenopausal and 40 postmenopausal women were diagnosed with AH. A medical checkup with 24 h monitoring of blood pressure (RR) and heart rate was undertaken (HR). The polymorphism of the D-loop and 12S rDNA region of mtDNA was examined. Changes in the nucleotide sequence of mtDNA were observed in 23% of the group of 100 women. The changes were identified in 91.3% of HV1 and HV2 regions, 60.9% of HV1 segments, 47.5% of HV2 regions, and 43.5% of 12S rDNA regions. The frequency of nucleotide sequence alterations in mtDNA was substantially higher in postmenopausal women (34%) than in premenopausal women (10.6%), p = 0.016. A higher frequency of changes in HV1 + HV2 sections in postmenopausal women (30.2%) compared to the premenopausal group (10.6%) was detected, p = 0.011. Only postmenopausal women were found to have modifications to the HV2 segment and the 12S rDNA region. After menopause, polymorphism in the mtDNA region was substantially more frequent in women with arterial hypertension than before menopause (p = 0.030; 37.5% vs. 11.5%). Comparable findings were observed in the HV2 and HV1 regions of the AH group (35% vs. 11.5%), p = 0.015, in the HV1 segment (25% vs. 11.5%), p = 0.529, and in the HV2 segment, 12S rDNA (25% vs. 0%). More than 80% of all changes in nucleotide sequence were homoplasmic. The mtDNA polymorphisms of the nucleotide sequence in the HV1 and HV2 regions, the HV2 region alone, and the 12S RNA coding sequence were associated with estrogen deficiency and a more severe course of arterial hypertension, accompanied by symptoms of adrenergic stimulation.

Environmental sponge sampling: We are only scraping the surface

Drains located in retail deli departments are known harborage points for pathogenic and spoilage microorganisms. Previous studies have used sequencing approaches to study the microbial consortia found in drains and biofilms in various food processing environments. None of these studies, however, have focused on retail. The primary objective of this study was to characterize the microbiome of retail deli drain sponge samples and drain biomass samples through shotgun metagenomic and 16S rRNA amplicon sequencing approaches. Sponge samples were collected from the surfaces of retail deli drain covers and biomass samples were harvested from inside deli drain trenches from fourteen retail delis in three major US cities. All samples were subjected to 16S rRNA gene sequencing, and shotgun metagenomic sequencing was performed on a subset of samples. In the majority of samples, Pseudomonas was the most abundant; the remaining genera differed by sample, city, and sequencing method. Common sanitizer tolerance genes (qacE∆1 and qacE) were observed in all biomass samples which were subjected to shotgun metagenomic sequencing. While mean alpha diversity indices were similar between biomass and sponge samples evaluated via 16S RNA amplicon sequencing, a greater range of diversity was observed between biomass scrapes than sponge samples. Beta diversity differed significantly (P < 0.01) between biomass scrapes and sponges. Additionally, some taxa, such as the opportunistic pathogen Elizabethkingia, were virtually absent from sponge samples, but present at low abundance in biomass scrape samples. While studies traditionally have focused on detection of specific microorganisms of interest, this study indicates that drain trenches may harbor microorganisms that are not observed through traditional methods of environmental sampling (i.e. surface sponge samples). Collection of drain biofilms or biomass scrapes and use of culture-independent approaches would provide a more complete picture of the deli drain microbiome.

A Blind-Identification Test on Criconema annuliferum (de Man, 1921) Micoletzky, 1925 Species Complex Corroborate the Hyper-Cryptic Species Diversity Using Integrative Taxonomy.

Ring nematodes are obligate ectoparasites on crops and natural herbaceous and woody plants, and some species are of economic importance and cause damage to roots of several crops. Recent integrative taxonomical analyses recognized the existence of two cryptic species within the Criconema annuliferum morphotype in Spain. In this study, we corroborated that morphometric, morphological and a multi-locus analysis (including the ribosomal markers D2-D3 expansion segments of 28S rRNA, ITS rRNA, 18S RNA, and the mitochondrial DNA cytochrome oxidase I gene) identified a new lineage clearly separated from C. annuliferum, C. paraannuliferum and C. plesioannuliferum. The new lineage was described herein as Criconema pseudoannuliferum sp. nov., confirming that C. annuliferum species complex species complex comprises a hyper-cryptic species complex. This research analysed soil samples from the rhizosphere of maritime pine (Pinus pinaster Ait.) forests in Bermeja-Crestellina Mountain, located at the western part of Málaga province, southern Spain. The integrative taxonomical analyses revealed the occurrence of a new cryptic species identified using females, males and juveniles with detailed morphology, morphometry and molecular markers, described herein as Criconema pseudoannuliferum sp. nov. All molecular markers (D2-D3, ITS, 18S and COI) were obtained from the same individual that was also used for morphological and morphometric analyses. This research demonstrated the hidden diversity within the C. annuliferum species complex species complex can reach to four lineages under ribosomal and mitochondrial gene markers for one morphospecies group, which includes four species, viz. C. annuliferum, C. paraannuliferum, C. plesioannuliferum, and C. pseudoannuliferum sp. nov. Criconema pseudoannuliferum sp. nov. was detected in moderate soil density in two maritime pine forests (5 and 25 nematodes/500 cm3 of soil) suggesting that does not cause damage to maritime pine.

Development of antagonistic yeasts for controlling black mold disease of onion

BackgroundThe present study aimed to examine the biocontrol efficacy of 28 yeast isolates against Aspergillus niger, the common pathogen of onion black mold disease. The antagonistic potential of yeast isolates against A. niger growth was investigated using a dual culture technique.ResultsFive yeast isolates, including 8 and 11, showed the highest inhibition effect on the mycelial growth of A. niger. Molecular analysis using 16S RNA identified strains 8 (AUN-AH14) and 11 (AUN-AH23) as Galactomyces geotrichum (JQ713185.1) and G. geotrichum (DQ849321.1), respectively. The culture filtrates of AUN-AH14 and AUN-AH23 at percentage concentrations of 20, 40, 60, and 80 were tested against the growth of A. niger. As a result, the lowest dry weight of the pathogen was obtained with culture filtrates of the two strains at concentrations of 60 and 80%.. Treatment of onion bulbs with formulation of antagonistic yeast isolates AUN-AH14 and AUN-AH23 and their corresponding cultural filtrates at 80% concentration significantly reduced the severity of black mold disease relative to the controls.ConclusionsThe most significant reduction in black mold severity was proved in yeast formulations of AUN-AH14 and AUN-AH23, followed by their cultural filtrates (CF-AUN-AH14 and CF-AUN-AH23). The shelf life of formulated yeast isolates began to gradually deteriorate after 5 months of storage at 4 °C.

Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin.

To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ13CDIC and TDS and lower SO42-, Fe3+ and NO3- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3- and SO42-, causing a decrease in the content of these two ions in the stagnant areas.

Molecular Identification of Bacteria Isolated from Marketed Sparus aurata and Penaeus indicus Sea Products: Antibiotic Resistance Profiling and Evaluation of Biofilm Formation.

Marketed fish and shellfish are a source of multidrug-resistant and biofilm-forming foodborne pathogenic microorganisms. Bacteria isolated from Sparus aurata and Penaeus indicus collected from a local market in Hail region (Saudi Arabia) were isolated on selective and chromogenic media and identified by using 16S RNA sequencing technique. The exoenzyme production and the antibiotic susceptibility patterns of all identified bacteria were also tested. All identified bacteria were tested for their ability to form biofilm by using both qualitative and quantitative assays. Using 16S RNA sequencing method, eight genera were identified dominated by Vibrio (42.85%), Aeromonas (23.80%), and Photobacterium (9.52%). The dominant species were V. natrigens (23.8%) and A. veronii (23.80%). All the identified strains were able to produce several exoenzymes (amylases, gelatinase, haemolysins, lecithinase, DNase, lipase, and caseinase). All tested bacteria were multidrug-resistant with a high value of the multiple antibiotic index (MARI). The antibiotic resistance index (ARI) was about 0.542 for Vibrio spp. and 0.553 for Aeromonas spp. On Congo red agar, six morphotypes were obtained, and 33.33% were slime-positive bacteria. Almost all tested microorganisms were able to form a biofilm on glass tube. Using the crystal violet technique, the tested bacteria were able to form a biofilm on glass, plastic, and polystyrene abiotic surfaces with different magnitude. Our findings suggest that marketed S. aurata and P. indicus harbor various bacteria with human interest that are able to produce several related-virulence factors.

Celiac Disease and a Gluten-Free Diet Lead to Loss of Methanobrevibacter from the Gut Microbiome

Introduction: The importance of the human microbiome has become well known in recent years. The microbiome contains a diverse number of organisms including bacteria, archaea, fungi, and protozoa, which when imbalanced, can lead to a variety of dysbioses. Celiac disease (CD) is a condition where the immune system responds to gluten, a protein found in wheat, leading to chronic inflammation in the small intestine. Studies have found that microbial dysbiosis is often associated with patients who have CD, but few have looked at how gluten affects the microbiome in comparison to CD. This research sought to identify microbiome changes between people with CD (on a gluten-free diet), those on a gluten-free diet (without CD), and a control group (without CD and a gluten-free diet). Methods: Twenty-nine eligible participants (screened via a survey) provided a single stool sample (12 CD, 8 gluten-free, and 9 control). The microbial DNA was extracted from the stool samples using the QIAamp PowerFecal DNA Kit (Qiagen) and the V3/V4 region of 16s RNA using the 600-cycleMiSeq kit (Illumina). Sequenced DNA was sent to the University of Utah for analysis. Changes in microbiome diversity were statistically analyzed using a Kruskal-Wallis analysis. Results: No change in alpha or beta diversity was seen between any study groups. In addition, significance was not observed in common phyla normally affected by CD (Firmicutes, Bacteroides, and Actinobacteria). However, a statistically significant difference was seen in the archaeal genera Methanobrevibacter, which was found only in the control group (p = 0.0212). Discussion: Previously reported changes in the microbiome of CD patients were not observed in this study. However, changes could be seen in the archaeal genius, Methanobrevibacter, which was found only control group at an abundance of 3.3%. Thus, when CD individuals were compared to healthy individuals with similar gluten-free diets there was little difference in gut microbial species suggesting that gluten-free diet may normalize CD-related microbiome changes. Conclusion: The absence of Methanobrevibacter from CD and gluten-free groups requires additional analysis to understand what role Methanobrevibacter plays in the microbiome and how a gluten-free diet may affect that role.

Valorization of Food Waste Slurry as Potential Candidate for Lipid Accumulation: A Concept of Oleaginous Bio-Refinery

In the current state of huge waste production and energy crisis, there is a need to find additional alternate energy resources and options for waste management. The present study was designed to measure the potential of different fruit wastes to serve as substrate for lipid accumulation in oleaginous bacteria. For this purpose, three novel bacterial strains (AF3, KM1 and KM10) isolated from the crude oil samples were systematically compared for their lipid accumulation potential using three types of waste including orange waste (OW), mango waste (MW) and apple waste (AW). Using waste as sole substrate, it was observed that maximum lipid accumulation by each strain was above 20%, which confirms that the bacteria belong to the oleaginous group. However, each bacterial isolate represented differential accumulative capacity with varying organic matter removal efficiency. Maximum lipid accumulation was achieved by KM10 (&gt;25%) with AW as substrate, and KM1 (&gt;24%) with MW as substrate; however, AF3 represented only 21% lipid accumulation using AW as substrate. Similarly, the maximum removal efficiency was recorded for KM10 in AW, followed by OW, where &gt;60% and &gt;50% of volatile solids (VS) removal, respectively, were achieved over the period of 7 days of incubation. This showed that the oleaginous strains also exhibit excellent waste treatment efficiency. The 16s RNA gene sequencing results showed that these KM1 and KM10 strains were Serratia surfactantfaciens and Serratia liquefaciens. In the end, a circular economy model was presented to highlight the significance of the mechanisms, which offers dual benefits over the linear economy model. Overall, the findings of the present study revealed that the novel oleaginous strains not only provide considerable lipid accumulation, but are simultaneously capable of low-cost waste treatment.

Microbial Communities of Peaty Permafrost Tundra Soils along the Gradient of Environmental Conditions and Anthropogenic Disturbance in Pechora River Delta in the Eastern European Arctic

Microbial communities play crucial roles in the global carbon cycle, particularly in peatland and tundra ecosystems experiencing climate change. The latest IPCC assessments highlight the anthropogenic changes in the Arctic peatlands and their consequences due to global climate change. These disturbances could trigger permafrost degradation and intensification of the biogeochemical processes resulting in greenhouse gas formation. In this study, we describe the variation in diversity and composition of soil microbial communities from shallow peat tundra sites with different anthropogenic loads and applied restoration interventions in the landscape of remnant fragments of terraces in the Pechora River delta, the Russian Arctic, Nenets Autonomous Okrug. The molecular approaches, including quantitative real-time PCR and high-throughput Illumina sequencing of 16S RNA and ITS, were applied to examine the bacterial and fungal communities in the soil samples. Anthropogenic disturbance leads to a significant decrease in the representation of Acidobacteria and Verrucomicrobia, while the proportion and diversity of Proteobacteria increase. Fungal communities in undisturbed sites may be characterized as monodominant, and anthropogenic impact increases the fungal diversity. Only the verrucomicrobial methanotrophs Methyloacifiphilaceae were found in the undisturbed sites, but proteobacterial methanotrophs Methylobacterium-Methylorubrum, as well as different methylotrophs affiliated with Methylophilaceae, and Beijerinckiaceae (Methylorosula), were detected in disturbed sites.

Isolation of Antimicrobial Active Compounds Producing Bacillus subtilis Strain from Bat Guano of Kashmir Cave, Pakistan

In this study, bacterial isolates form Bat guano of a lime stone cave capable of producing antibiotics are reported. Screening of bacterial strains was carried out from top, middle, and bottom layer of the guano sample. Out of 20 isolated strains, three showed antimicrobial activity against all tested ATTC strain of common bacterial (both gram positive and gram negative) and fungal species. 16s RNA gene sequencing of the strain showing maximum activity revealed the isolated strain as Bacillus subtilis. Optimum production of antimicrobial compounds took place in TSB medium after 72 h of incubation at 30 °C. FTIR of crude extract showed chemical similarity with bacitracin. GCMS analysis of the crude extract revealed a range of antimicrobial and anticancer compounds. It is concluded that Bacillus subtilis strain isolated from Bat Guano is a potential source of novel antimicrobial compounds of broad-spectrum nature and have inhibitory effects against potential pathogens.

Isolation of Pseudomonas aeruginosa from Persistent Bacterial Coinfection of a COVID-19 Patients with Molecular Detection of Antibiotics Resistance Genes.

Pseudomonas aeruginosa(P. aeruginosa) have a considerable risk to public health in the world, due to its high ability to develop resistance to different classes of antibiotics. It has been discovered as a prevalent coinfection pathogen that causes sickness exacerbation in COVID-19 patients. This study aimed to determine the prevalence of P. aeruginosa from COVID-19 patients in Al Diwaniyah province, Iraq and to identify its genetic resistance pattern. 70 clinical samples were obtained from severe cases of patients (RT-PCR positive for SARS-COV-2 on a nasopharyngeal swab) who attended Al Diwaniyah Academic Hospital. 50 P. aeruginosa bacterial isolates were detected via microscopic examination, routine cultured and biochemical testing, then validated by the VITEK-2 compact system. VITEK reported 30 positive results, which later confirmed through molecular detection using 16s RNA specific for detection and a phylogenetic tree.20 isolates had positive PCR findings and 5 isolates submitted to GenBank with accession numbers OL314557.1, OL314556.1, OL314555.1, OL314554.1, OL314553.1.For antibiotic resistance genes, the number of the isolates containing blaOXA-1 and blaCTX-M 18 (90 percent) and 16 (80 percent) respectively. To study its adaptation in a SARS-CoV-2 infected environment, genomic sequencing investigations were undertaken with phenotypic validation. In conclusion, we demonstrate that multidrug resistant P. aeruginosa play an important role in in vivo colonization in COVID-19 patients and could be one of the causes of death of these patients which indicates the great challenge to clinicians in the facing of this serious disease.

Análisis y caracterización de poblaciones bacterianas solubilizadoras de P en un ensayo de larga duración con diferentes secuencias de cultivo

It is well known that different soil use and management systems affect the abundance, activity and composition of the soil microbial community. In this work, the behavior of cultivable bacterial populations and, in particular, P (PSB) solubilizing bacteria in soil samples from a long-term trial with different culture sequences was studied. The results obtained show that the clearing and subsequent agricultural use after 11 years generated a decrease in the population of cultivable bacteria in general, and of P-solubilizing bacteria in particular, with respect to the pristine soil. Isolates with high P solubilization efficiency were obtained from the soils from the different rotations. These efficient isolates were taxonomically classified by 16S RNA analysis as belonging to the genera Bacillus, Paenibacillus, Pseudomonas and Xanthomonas. In particular, the characterization of the culture supernatants of the isolates Pseudomonas koreensis and Paenibacillus pabuli showed they are producers of organic acids. The combined inoculation tests of these two strains on maize plants in a culture chamber revealed a synergistic effect on the growth promotion of this species. The results presented here suggest that although PSB populations are more numerous in pristine soils, certain long-term crop rotations favor the increase of more efficient solubilizing bacteria, an aspect that should be considered when designing future search strategies for potential bioinoculants.

Controlled manipulation of the gut microbiome improves intracortical microelectrode performance.

Intracortical microelectrode arrays (MEAs) record neuronal action potentials in the brain and can be paired with external systems to provide motor function rehabilitation to those with disabilities. Unfortunately, recording quality of MEAs consistently declines over the course of weeks to months compromising device utility. Neuroinflammation from persistent indwelling of MEAs is considered a significant contributor to the decline in recording performance. Recent evidence suggests that the gut microbiome may play a role in brain health possibly via bacteria-specific metabolites or microbiota infiltrating through the blood-brain barrier. Therefore, we hypothesize that altering the gut microbiome in mice via oral antibiotics or probiotics could change the microbiome composition in both the brain and gut, affecting neuroinflammation and MEA performance. Here, mice implanted with an MEA device for 12 weeks were treated with either antibiotics, probiotics, or normal diet to modulate gut microbiome composition. Biweekly neural recording sessions indicated temporal differences in MEA recording performance. Acutely (Weeks 1-5), antibiotic-treated mice (79% active electrode yield, AEY) and probiotic-treated mice (74% AEY) showed significantly better MEA performance than control (69% AEY). Probiotic significantly outperformed antibiotic sub-chronically (Weeks 6-11) and chronically (Weeks 12+). Differential changes to 16S RNA composition in stool and brain tissue suggested treatment-specific changes at the neural implant site. Culturing of explanted brain tissue indicated that live gut-derived bacteria were differentially found in the brain after implantation and treatment. Transcriptomic and proteomic analysis on brain tissue is underway to understand the correlation between MEA performance, microbiome composition, and neuroinflammation following MEA implantation and treatment. At minimum, our data suggest a connection between microbiome composition and recording performance. Such evidence provides a novel means for understanding and improving the lifetime of MEA devices to be used chronically in humans.

A prospective translational study investigating the association of gut microbiome (GM) diversity with pathological complete response (pCR) after neoadjuvant treatment in early stage rectal and esophageal cancers.

TPS819 Background: The gut microbiome (GM) is thought to influence host immunity by modulating multiple immunologic pathways. Studies have suggested that dysbiosis of the GM confers a predisposition to certain malignancies and influences response to immune checkpoint inhibitors. However, little is known about how the GM diversity influences complete pathological response to neoadjuvant therapy in gastrointestinal (GI) tumours. We hypothesize that a more diverse GM constitution at baseline will lead to improved pathological response at the time of definitive surgery. Methods: We designed a cross-institutional multi-center translational study investigating the impact of the GM diversity on the efficacy of neoadjuvant therapy in GI cancers by assessing its association with pathological response. The study population will consist of patients with an early-stage rectal or esophageal cancer due to commence neoadjuvant therapy (including chemotherapy and chemoradiation) and planned for definitive surgery. Patients who received prior chemotherapy/monoclonal antibodies/immune checkpoint inhibitors or radiation will be excluded. The study assessments will include fecal sampling of the GM prior to neoadjuvant therapy, upon completion and again six months post completion of therapy. Fecal samples will be analysed by 16S RNA sequencing. Pathological response will be examined at time of surgery and patients will be classified as responders (complete pathological response) or non-responders. The primary endpoint of the study is to examine the association between the GM diversity and pathological response. 120 patients will be recruited over 18 months. Results: Species richness (Alpha Diversity) will be analysed using the Shannon diversity index and Jaccard similarity index to calculate beta diversity. Classification and clustering analysis will be performed with Principal Component Analysis (PCA) and Random Forest analysis. Comparison of taxa or functions between clinical cohorts will be performed using the two tailed Z test and corrected using the false discovery rate to determine Q-values. The association between GM and complete pathological response will be examined using logistic regression analysis adjusting for potential confounding factors. Adjusted odds ratios (OR) and 95% confidence intervals will be presented. Conclusions: This study will show preliminary insights into the role of GM as a potential biomarker for neoadjuvant therapy efficacy in patients with GI cancers. Recruitment is on-going.

DOP51 Mucosa-associated microbial signatures associate with objective response prior to the start of anti-TNFα but not vedolizumab or ustekinumab in Crohn’s disease patients

Abstract Background Crohn’s disease (CD) is a complex immune-mediated disease of the gastrointestinal tract where the gut microbiome plays an important role. Current biological treatment options in CD include the anti-TNFα agents adalimumab (ADA) and infliximab (IFX), vedolizumab (VDZ), and ustekinumab (USTE). Finding biomarkers to predict therapy response is still a clinical unmet need, as the majority of CD patients fail to reach endoscopic remission within 1 year of treatment. While the majority of studies focus on fecal samples, mucosa-adherent bacterial signature could bring forth stable biomarkers. In this study, we sought to identify signatures of the adherent microbiome in intestinal biopsies aimed at differentiating responders (R) from non-responders (NR), prior to the start of biological treatment. Methods We prospectively collected paired ileal and colonic biopsies (stored snapfrozen in -80 ºC) from adult CD patients scheduled to start anti-TNFα (IFX and ADA), VDZ and USTE treatment during baseline endoscopies. After 6-12 months of follow-up, patients were classified as either R or NR based on endoscopic response (≥50% reduction in SES-CD score) in combination with steroid-free clinical response (≥3 point drop in HBI or HBI ≤4) and/or biochemical response (≥50% reduction in C-reactive protein (CRP) and fecal calprotectin or a basal CRP ≤5 g/mL and fecal calprotectin ≤250 µg/g). Microbiome composition of the biopsies was determined using 16S RNA gene V3V4 amplicon sequencing. Results For the anti-TNFα cohort, we included in total 36 CD patients (21R and 18 NR), for VDZ cohort a total of 44 patients (28 R and 16 NR) and for USTE cohort a total of 40 patients (20R and 20 NR).When comparing α-diversity and β-diversity between R and NR, we did not find significant differences in ileal and colonic samples at baseline for the VDZ and USTE cohorts. Notable, for the anti-TNFα cohort (table 1), we obtained significant differences when comparing α-diversity (p=0.028) and β-diversity between R and NR. We demonstrated differences between colonic R and NR in taxa abundance for ASVs associated with the phyla Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria (figure 1). Furthermore, ASVs associated with Firmicutes, Bacteroidetes, Actinobacteria are different in abundance between ileal R and NR (figure 2). Figure 1: Differential taxa abundance colonic R vs NR anti-TNFα Figure 2: Differential taxa abundance ileal R vs NR anti-TNFα Figure 3: graphical summary Conclusion Here, we investigated the microbial signature of R and NR before the start of treatment of three separate cohorts and we demonstrated that the mucosa-associated microbiome differentiates R and NR to anti-TNFα therapy. Further analyses as part of the EPIC Pioneer study, are ongoing.

Characterization of Autochthonous Strains from the Cecal Content of Creole Roosters for a Potential Use as Probiotics.

Five strains (CLP2, CLP3, CLP4, CLP5, and CLP6) were isolated from the cecal content of Creole roosters fed without antibiotic growth promoters. Biochemical and morphological tests (negative catalase and oxidase) confirmed the presence of lactic acid bacteria. Additionally, considering the 16s RNA, Lactobacillus vaginalis (CLP2, CLP3, CLP5, and CLP6) and Lactobacillus reuteri (CLP4) were identified. All strains (mainly CLP4 and CLP5) showed variable and significant growth (p < 0.001) at different levels of pH. Likewise, all bacterial cultures were quantified at 42 °C, although only strains CLP4 and CLP5 managed to grow at 30 °C. Additionally, the CLP4, CLP5, and CLP6 strains grew from 0.05 to 0.30% of biliary salts. However, only the CLP4 isolate grew at different concentrations of NaCl (2-10%), and CLP5 grew at 2% NaCl. The CLP4 strain was able to inhibit the in vitro growth of enterobacteria such as Escherichia coli ATCC® 11775TM, Salmonella Typhimurium ATCC® 14028TM, and Clostridium perfringens ATCC® 13124TM. In addition, CLP4 had lower sensitivity in the presence of amoxicillin and tetracycline compared to these pathogenic bacteria. Considering these in vitro results, it is necessary to carry out in vivo studies with the CLP4 strain to test the hypothesis of its probiotic effect in poultry.

Exploring the interrelationship between the skin microbiome and skin volatiles: A pilot study

Unravelling the interplay between a human’s microbiome and physiology is a relevant task for understanding the principles underlying human health and disease. With regard to human chemical communication, it is of interest to elucidate the role of the microbiome in shaping or generating volatiles emitted from the human body. In this study, we characterized the microbiome and volatile organic compounds (VOCs) sampled from the neck and axilla of ten participants (five male, five female) on two sampling days, by applying different methodological approaches. Volatiles emitted from the respective skin site were collected for 20 min using textile sampling material and analyzed on two analytical columns with varying polarity of the stationary phase. Microbiome samples were analyzed by a culture approach coupled with MALDI-TOF-MS analysis and a 16S ribosomal RNA gene (16S RNA) sequencing approach. Statistical and advanced data analysis methods revealed that classification of body sites was possible by using VOC and microbiome data sets. Higher classification accuracy was achieved by combination of both data pools. Cutibacterium, Staphylococcus, Micrococcus, Streptococcus, Lawsonella, Anaerococcus, and Corynebacterium species were found to contribute to classification of the body sites by the microbiome. Alkanes, esters, ethers, ketones, aldehydes and cyclic structures were used by the classifier when VOC data were considered. The interdisciplinary methodological platform developed here will enable further investigations of skin microbiome and skin VOCs alterations in physiological and pathological conditions.

MoMaf1 Mediates Vegetative Growth, Conidiogenesis, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae.

In eukaryotes, Maf1 is an essential and specific negative regulator of RNA polymerase (Pol) III. Pol III, which synthesizes 5S RNA and transfer RNAs (tRNAs), is suppressed by Maf1 under the conditions of nutrient starvation or environmental stress. Here, we identified M. oryzae MoMaf1, a homolog of ScMaf1 in budding yeast. A heterogeneous complementation assay revealed that MoMaf1 restored growth defects in the ΔScmaf1 mutant under SDS stress. Destruction of MoMAF1 elevated 5S rRNA content and increased sensitivity to cell wall agents. Moreover, the ΔMomaf1 mutant exhibited reduced vegetative growth, conidiogenesis, and pathogenicity. Interestingly, we found that MoMaf1 underwent nuclear-cytoplasmic shuffling, through which MoMaf1 accumulated in nuclei under nutrient deficiency or upon the interaction of M. oryzae with rice. Therefore, this study can help to elucidate the pathogenic molecular mechanism of M. oryzae.