16S RNA Gene Research Articles

First report on the molecular prevalence and associated risk factors of Eimeria spp. in dairy cattle in Khon Kaen, Thailand.

Bovine coccidiosis, caused by the protozoa Eimeria, is an important parasitic cattle disease that affects animal health and has economic impact worldwide. This study was conducted to report the first molecular prevalence and genetic diversity of Eimeria spp. in dairy cattle in Khon Kaen province, Thailand, and to identify the risk factors associated with Eimeria spp. infection. From July 2020 to October 2021, 296 fecal samples were collected from dairy cattle divided into three age groups, including <3-month-old calves, 3-month-old to 1-year-old calves, and >1-year-old cattle. Eimeria spp. were identified by multiplex polymerase chain reaction (PCR) amplifying 18S RNA gene and confirmed by DNA sequencing. Information regarding all associated risk factors was collected using questionnaires and analyzed using logistic regression tests in the Statistical Package for the Social Sciences program. Polymerase chain reaction results showed that 104 (35.13%) of 296 samples were positive for Eimeria spp. The <3-month-old calves (46.51%) had the highest infection rate. Moreover, multiplex PCR identified five species of Eimeria, namely, Eimeria bovis (32.69%), Eimeria zuernii (18.26%), Eimeria alabamensis (5.76%), Eimeria ellipsoidalis (3.84%), and Eimeria cylindrica (2.88%). An association was observed between risk factors and Eimeria spp. incidence (p < 0.05). DNA sequencing revealed the similarity of each Eimeria spp. with 91%-100% nucleotide identity. Phylogenetic tree analysis demonstrated the close relationships of clusters of E. bovis and E. zuernii, E. ellipsoidalis, and E. cylindrica and another cluster of E. alabamensis. The results confirm that Eimeria spp. are commonly found in dairy cattle, especially calves. The molecular test could be powerful for species identification. This study also provides epidemiological information for developing future strategies to control bovine coccidiosis.

Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain.

Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed thatAcinetobacter sp. strain P1 exhibited the highest homology with theAcinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.

Effects of sample collection and storage methods on fecal bacterial diversity in California ground squirrels (Otospermophilus beecheyi)

Abstract Measures of fecal bacterial abundance and taxonomic composition are commonly used as proxies for gut microbial diversity in studies of free-living mammals. Because methods of sample collection and storage may affect measures of bacterial diversity, we evaluated the effects of several procedures on fecal bacterial diversity in a free-living population of California ground squirrels (Otospermophilus beecheyi). Replicate fecal samples from 12 adult female squirrels were collected either from the soil beneath traps in which individuals had been captured or from tubs placed under squirrels during handling. Samples were then either frozen immediately in liquid nitrogen or stored on ice for several hours before being transferred to a −80°C freezer. Sequencing of the bacterial 16s RNA gene revealed no differences among methods with regard to sequence read depth (number of sequences recovered per animal) or alpha (within-individual) diversity of bacterial taxa. While our collection-storage procedures had a significant effect on one of the metrics of beta (among-individual) bacterial diversity examined, this effect was small compared to that of individual identity. Date of sample collection affected alpha and beta diversity; samples collected only 1 week apart differed significantly in bacterial diversity. Overall, these findings suggest that the collection and storage methods employed yield generally comparable information and are capable of capturing potentially important patterns of fecal bacterial composition and diversity in free-living mammals.

A multiphasic approach to solve misidentification of Cutibacterium acnes as Atopobium vaginae during routine bacterial screening of platelet concentrates using the VITEK 2 system.

Skin flora bacteria, such as Cutibacterium acnes , are the predominant contaminants of blood products used for transfusion. Platelet concentrates (PCs), a therapeutic product used to treat patients with platelet deficiencies, are stored at ambient temperature under agitation, providing ideal conditions for bacterial proliferation. At Canadian Blood Services, PCs are screened for microbial contamination using the automated BACT/ALERT culture system. Positive cultures are processed and contaminating organisms are identified using the VITEK 2 system. Over a period of approximately 2 years, several PC isolates were identified as Atopobium vaginae to a high level of confidence. However, since A. vaginae is associated with bacterial vaginosis and is not a common PC contaminant, a retrospective investigation revealed that in all cases C. acnes was misidentified as A. vaginae . Our investigation demonstrated that the media type used to grow PC bacterial isolates can have a significant impact on the results obtained on the VITEK 2 system. Furthermore, other identification methods such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALD-TOF MS) and PCR amplification of the 16S RNA gene were only partially successful in the identification of C. acnes . Therefore, our findings support a multiphasic approach when PC isolates are identified as A. vaginae by the VITEK 2 system for proper identification of C. acnes using macroscopic, microscopic and other biochemical analyses.

Development of a multiplex qRT-PCR assay for detection of classical swine fever virus, African swine fever virus, and Erysipelothrix rhusiopathiae.

Classical swine fever virus (CSFV), African swine fever virus (ASFV), and Erysipelothrix rhusiopathiae (E. rhusiopathiae) remain endemic in many parts of China. Co-infections make distinguishing their clinical symptoms and pathological changes difficult. This study developed a multiplex real-time quantitative reverse transcription polymerase chain reaction (multiplex qRT-PCR) that can simultaneously detect CSFV, ASFV, and E. rhusiopathiae. Three sets of primers and probes were designed to target the CSFV 5΄ untranslated region, ASFV p72 gene, and E. rhusiopathiae 16sRNA gene. Multiplex qRT-PCR for simultaneous differential detection of these three pathogens was developed after optimizing reaction parameters such as annealing temperature, primer and probe concentrations, amplification cycles, etc. The multiplex qRT-PCR could detect CSFV, ASFV, and E. rhusiopathiae simultaneously but could not amplify other porcine pathogens. The assay's limit of detection (LOD) was 2.89 × 102 copies/μL for CSFV, ASFV, and E. rhusiopathiae. All correlation coefficients (R2) at higher than 0.99, and the amplification efficiency was 98, 90, and 84%, respectively. All correlation coefficients (R2) were higher than 0.99, and the efficacy of amplification was 84%. In a repeatability test utilizing standard recombinant plasmids, the intra- and inter-assay coefficients of variation (CVs) were less than 2.27 and 3.79 percent, respectively. Lastly, 150 clinical samples were used to evaluate the assay's applicability in the field. The positive rates of CSFV, ASFV, and E. rhusiopathiae were 1.33%, 0, and 3.33%, respectively. And no co-infection among the three pathogens was found. The concordance rate between the multiplex qRT-PCR and single-plex commercial PCR kits reached 100%. This study's multiplex qRT-PCR could provide a rapid, sensitive, and specific method for the simultaneous and differential detection of CSFV, ASFV, and E. rhusiopathiae.

Antimicrobial activity of whey milk and their fractions against Staphylococcus pasteuri clinical strain

The antibacterial activity of Whey Milk and its fractions were studied against one hundred bacteria strains isolated and screened from various patients at the University Hospital of Zagazig, Sharkia Province, Egypt. F2 fraction of Whey Milk has shown the highest degree of antibacterial activity against the pathogenic bacteria A63 isolated from the wound. Buffalo whey (BW) was hydrolyzed with papain followed by fractionation using size exclusion chromatography (SEC). The fractionation profile of BWH showed three major peaks in Size exclusion chromatography, SECF1, SECF2, and SECF3 after 3h. F2 is the most active fraction and has faster migration than HP, F1, and F3 and may have higher positive charges on Urea-PAGE towards the cathode direction. FTIR spectrum analysis of the F2 fraction of whey protein demonstrates the occurrence of distinctive functional groups, such as Alkanes, alcohols, phenols, flavonoids, alkenes, anhydrides, and halo compounds. The biochemical characters and the 1.5 Kb 16S RNA gene's nucleotide sequence of the most potent stain showed 99% similarity with Staphylococcus pasteuri. Our results showed that the ability of nanoparticles of whey to inhibit pathogenic bacteria decreases compared to raw whey and its fractions. Cellular deformation and partial and total lysis of cell components were seen in Staphylococcus pasteuri treated with whey F2 fraction under Transmission Electron Microscopy (TEM).

Systematic review–how do we identify urinary tract infections today?

Standard urine culture is still considered a gold standard in the identification of Urinary Tract Infections (UTIs), but is time-consuming and in approximately 20% of patients with UTI symptoms produces false-negative results. Medical and scientific communities are in search of a faster, more accurate, yet affordable method with high clinical utility. As a supplement to standard culture in routine practice Urine Flow Cytometer (UFC) screening method is used, in order to detect negative urine culture samples. This allows for shortening issuing time for sterile urine culture reports and the cost of the analysis itself. In addition, urine dipstick tests and microscopic examinations of urine sediment can also be performed in biochemical laboratories but are usually preceded by urine culture. Nowadays, advanced methods such as proteomics and genomics are used to identify pathogens causing UTIs but are still used mainly for scientific purposes and rarely in clinical practice. From genomic methods PCR, 16S rRNA gene sequencing, and metagenome sequencing are being researched. PCR is great for targeted diagnostics, 16S RNA gene amplification can determine bacterial genera and their abundance, but is not good for in-depth species analysis, while metagenomics is the most comprehensive and unbiased method. The proteomics field also offers several methods for microbial identification, with MS as the leading one. Clinical applications of MS platforms usually imply MALDI-TOF MS analyzers which produce a characteristic spectrum called peptide mass fingerprint or more present for scientific purposes LC-MS/MS-based peptide sequencing.

Significance of the determination of DNA load of drug-resistant mycoplasma pneumoniae and 23sRNA gene mutation locus in children

Purpose: To determine the significance of the detection of Mycoplasma pneumoniae (MP)-DNA load and 23sRNA gene mutation locus in children with drug-resistant MP pneumonia. &#x0D; Methods: A total of 158 children with MP pneumonia received drug sensitivity tests. The patients were divided into resistance group and non-resistance group. The MP-DNA load index (MPLI) and mutation rate of 23sRNA gene at 2063 locus were assessed and compared between the two groups: the MPLI-negative group and the MPLI-positive group, based on whether MPLI was greater than 6.12. The association of MPLI of all the patients and the 23sRNA gene mutation at 2063 locus in the resistance group, as well as clinical indicators were analyzed. &#x0D; Results: The MPLI of the resistance group was lower than that of the non-resistance group. In the MPLI-positive group, the duration of disease, defervescence time, disappearance time of cough and expectoration, disappearance time of chest opacity, and length of stay were all longer than those of the MPLI-negative group, while the proportion of cases with extrapulmonary complications and the white blood cell (WBC) count were higher than those of the MPLI-negative group. The mutation rate of 23sRNA gene at 2063 locus in the resistance group was higher than that in non-resistance group (p &lt; 0.05). The defervescence time, disappearance time of cough and expectoration, disappearance time of chest opacity and length of stay were longer in the mutation-positive group than those in the mutation-negative group (p &lt; 0.05). &#x0D; Conclusion: The mutation rate of 23sRNA gene at 2063 locus is higher in children with drug-resistant MP pneumonia. Furthermore, low MPLI and 23sRNA gene mutations at 2063 locus are associated with the duration of disease, disappearance time of clinical symptoms and other clinical indicators.

Characterization of high-yield Bacillus subtilis cysteine protease for diverse industrial applications.

Bacterial proteases have extensive applications in various fields of industrial microbiology. In this study, protease-producing organisms were screened on skimmed milk agar media using serial dilution. Through microbial biomass production, biochemical tests, protease-specific activity, and 16s RNA gene sequencing, the isolates were identified as Bacillus subtilis and submitted to NCBI. The strain accession numbers were designated as A1 (MT903972), A2 (MT903996), A4 (MT904091), and A5 (MT904796). The strain A4 Bacillus subtilis showed highest protease-specific activity as 76,153.84 U/mg. A4 Bacillus subtilis was unaffected by Ca2+, Cu2+, Fe2+, Hg2+, Mg2+, Na, Fe2+, and Zn2+ but was inhibited by 80% by Mn2+ (5mM). The protease activity was inhibited by up to 30% by iodoacetamide (5mM). These findings confirm the enzyme to be a cysteine protease which was further confirmed by MALDI-TOF. The identified protease showed 71% sequence similarity with Bacillus subtilis cysteine protease. The crude cysteine protease significantly aided in fabric stain removal when added to a generic detergent. It also aided in the recovery of silver from used X-ray films and de-hairing of goat skin hides and showed decent application in meat tenderization. Thus, the isolated cysteine protease has high potential for industrial applications.

Profiling of adrenal corticosteroids in blood and local tissues of mice during chronic stress

Stress increases plasma concentrations of corticosteroids, however, their tissue levels are unclear. Using a repeated social defeat paradigm, we examined the impact of chronic stress on tissue levels of corticosterone (CORT), progesterone (PROG), 11-deoxycorticosterone (11DOC) and 11-dehydrocorticosterone (11DHC) and on gut microbiota, which may reshape the stress response. Male BALB/c mice, liquid chromatography-tandem mass spectrometry and 16S RNA gene sequencing were used to screen steroid levels and fecal microbiome, respectively. Stress induced greater increase of CORT in the brain, liver, and kidney than in the colon and lymphoid organs, whereas 11DHC was the highest in the colon, liver and kidney and much lower in the brain and lymphoid organs. The CORT/11DHC ratio in plasma was similar to the brain but much lower in other organs. Stress also altered tissue levels of PROG and 11DOC and the PROG/11DOC ratio was much higher in lymphoid organs that in plasma and other organs. Stress impacted the β- but not the α-diversity of the gut microbiota and LEfSe analysis revealed several biomarkers associated with stress treatment. Our data indicate that social defeat stress modulates gut microbiota diversity and induces tissue-dependent changes in local levels of corticosteroids, which often do not reflect their systemic levels.

Genetičke i genomske (molekularne) dijagnostičke metode u identifikaciji uzročnika infekcija mokraćnog sustava i urinarne mikrobiote

Standard urine culture (SUC) is a widespread diagnostic test. According to various guidelines, SUC is not a recommended first-line diagnostic tool for uncomplicated urinary tract infections (UTIs). However, its results are valuable in patients with complicated UTIs, hospitalized patients, and those who failed empirical antibiotic therapy. The emergence of antibiotic resistance has reaffirmed the urine culture as the gold standard in UTI workup. Nevertheless, turn-around-time and cost-effectiveness of SUC are the main incentives for continuous exploration of new, faster, and more sensitive procedures for evaluating the count and species of microorganisms and their susceptibility to antibiotics. Therefore, we considered it important to write a review that analyzes the advantages and disadvantages of state-of-the-art UTI diagnostics. We aim to compare standard cultivation methods with diagnostic modalities based on multiplex PCR, 16S RNA genes sequencing, and next-generation sequencing suitable for analyzing whole urinary microbiomes.

Preliminary evidence for developing safe and efficient fecal microbiota transplantation as potential treatment for aged related cognitive impairments.

Recent studies have reported that gut microbiota is closely associated with cognitive fuction. Fecal microbiota transplantation (FMT) may be a potential treatment for cognitive impairment, but its efficacy in patients with cognitive impairment is unknown. This study aimed to investigate the safety and efficacy of FMT for cognitive impairment treatment. Five patients aged 54-80 years (three women) were enrolled in this single-arm clinical trial from July 2021 to May 2022. The Montreal Cognitive Assessment-B (MoCA-B), Activities of Daily Living (ADL), and the cognitive section of the Alzheimer's Disease Assessment Scale (ADAS-Cog) were assessed at days 0, 30, 60, 90, and 180. Additionally, stool and serum samples were obtained twice before FMT was administered and six months after the treatment. The structure of fecal microbiota was analyzed by 16S RNA gene sequencing. Serum samples were analyzed for metabolomics and lipopolysaccharide (LPS)-binding proteins by liquid chromatography-mass spectrometry and enzyme-linked immunosorbent assay, respectively. Safety was assessed based on adverse events, vital signs, and laboratory parameters during FMT and the follow-up period. The MoCA, ADL, and ADAS-Cog scores of patients with mild cognitive impairment (patients C and E) after FMT were improved or maintained compared with those before transplantation. However, patients with severe cognitive impairment (patients A, B, and D) had no worsening of cognitive scores. Fecal microbiota analysis showed that FMT changed the structure of gut microbiota. The results of serum metabolomics analysis suggested that there were significant changes in the serum metabolomics of patients after FMT, with 7 up-regulated and 28 down-regulated metabolites. 3b,12a-dihydroxy-5a-cholanoic acid, 25-acetylvulgaroside, deoxycholic acid, 2(R)-hydroxydocosanoic acid, and P-anisic acid increased, while bilirubin and other metabolites decreased. KEFF pathway analysis indicated that the main metabolic pathways were bile secretion and choline metabolism in cancer. No adverse effects were reported throughout the study. In this pilot study, FMT could maintain and improve cognitive function in mild cognitive impairment by changing gut microbiota structure and affecting serum metabolomics. Fecal bacteria capsules were safe. However, further studies are needed to evaluate the safety and efficacy of fecal microbiota transplantation. ClinicalTrials.gov Identifier: CHiCTR2100043548.

Physicochemical Properties, Heavy Metal Composition, and Metal Resistant Microorganisms Associated with Gold Mine Tailings in Jebba, Nigeria

Mine tailings are a source of unique microorganisms with novel characteristics. This study aims to determine the chemical composition of the soil and water from different locations of an active artisanal gold mine and the microorganisms associated with the mine tailings. The physiochemical analysis of tailings soil and water, HM species, and their carcinogenic and non-carcinogenic effects were determined. Heavy metal resistant bacteria (HMRB) were then isolated using nutrient agar supplemented with metals. The results showed that pH and temperature of the soil and water samples ranged between 6.2- 6.6 and 29–30 °C respectively. The estimated incremental lifetime cancer risk (ILCR) from one location was 7.9E − 6 was the highest. The HMs detected includes Arsenic (As), Mercury (Hg), Cadmium (Cd), and Lead (Pb). Twenty-one HMRB were isolated and they are putatively identified as Staphylococcus spp., Bacillus sp., Salinicoccus halodurans, Staphylococcus chromogenes, Paenibacillus cellulositrophicus, Paenibacillus residui, Sporosarcina globispora, and Streptococcus sp. Analysis of the 16S RNA genes sequences revealed that isolate MS2 has 98.01% similarity to Aneurinibacillus aneurinilyticus. The presence and levels of HMs elucidates the high risk of cancerous and non-cancerous effects borne by artisan gold miners. The isolated HMRB can be further analyzed for possible bioremediation of the site.

Abstract 3044: Integrative gut microbiome analysis of human and mouse prostate cancer

Abstract Gut microbes are intricately involved in maintaining normal physiology and homeostasis and have become a major area of study to determine their relevance in human disease. In cancer, alterations to gut microbiota has been associated to resistance to chemo- and immuno-therapy, whereas supplementation with specific taxa improves antitumor treatment responses. Mouse models have been essential to study disease biology and drug discovery. However, mice are fundamentally quite different from humans, thus, questions have arisen regarding their utility as pertinent tools to study microbial influences and their impact on human disease. To address these questions, we have performed a cross-species comparative analysis of the fecal microbiota from a human cohort of prostate cancer patients and a preclinical mouse model of prostate cancer. Microbiota composition was determined by 16s RNA gene sequencing on stool samples from tumor-bearing prostate-specific conditional Pten-knockout and disease-free wildtype mice and 16s RNA gene sequencing data from a human cohort of patients with suspected prostate cancer was used. Human cases were assigned to no cancer and cancer groups based on diagnosis from prostate biopsy and as low-risk (negative biopsy of Gleason grade &amp;lt;3) or high-risk (Gleason grade ≥3). Community composition differed significantly between stool samples of cancer and disease-free individuals in mice but not humans. Operational taxonomic units (OTUs) corresponding to taxa associated with cancer in both mice and humans included Odoribacter spp. and Desulfovibrio spp. Comparing the profiles predicted with Tax4Fun revealed KEGG metabolic pathways associated prostate cancer. Pathways enriched in cancer bearing-mice and that are also associated in patients with prostate cancer included folate biosynthesis, biotin metabolism and ubiquinone &amp; other terpenoid-quinone biosynthesis. Carbon metabolism was a pathway discordant between high-risk prostate cancer patients and cancer bearing mice. Although the basal composition of gut microbes differed between humans and mice, the functional microbiome showed greater similarities. Our cross-species comparative analysis shows that gut microbial dysbiosis is connected to prostate cancer provides additional insights into the biological processes involved. This study provides additional data that may help to bridge the gap between humans and mice. Citation Format: Chisato Wakamori, Marco A. De Velasco, Yurie Kura, Naomi Ando, Noriko Sako, Kazutoshi Fujita, Kazuko Sakai, Makoto Matsushita, Eri Banno, Yasunori Mori, Masahiro Nozawa, Mitsuhisa Nishimoto, Kazuhiro Yoshimura, Norio Nonomura, Kazuto Nishio, Hirotsugu Uemura. Integrative gut microbiome analysis of human and mouse prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3044.

Identification and treatment of Strongyloides cebus in captive ring-tailed lemurs (Lemur catta) in the midwestern United States

Strongyloides spp. are parasitic enteric nematodes that infect a variety of hosts. While the Strongyloides spp. that affect humans, apes, and Old World primates have been previously identified, this genus has not been as fully investigated in prosimian species such as ring-tailed lemurs (Lemur catta). A high burden (4+) of larvated eggs and larvae were identified in the fecal samples of two captive ring-tailed lemurs during routine intake examination at a zoo in the midwestern United States. Conventional PCR targeting the 18S RNA gene of nematodes was used identified the parasite as Strongyloides cebus. The lemurs were initially treated with 0.2mg/kg ivermectin orally twice, two weeks apart. Repeat fecal sampling showed persistent, but decreased eggs and larvae from 4+ to 3+. Ivermectin treatment was repeated with the addition of fenbendazole at 50mg/kg orally once daily for 3days. No parasite stages were seen on fecal samples one week and six weeks after the last ivermectin indicating successful clearance of the infection.

Isolation and Identification of Seaweed-Associated Bacteria and Their Antibacterial Activity against Skin Disease Agents

Bacteria associated with marine organisms have become the focus of worldwide research for their potential to generate bioactive substances, such as antibacterial compounds. This study aimed to identify the antibacterial activity of seaweed-associated bacteria in Teluk Awur Jepara, Indonesia, against Propionibacterium acnes and Staphylococcus epidermidis. Three seaweed species, Caulerpa racemosa, Padina minor, and Halimeda opuntia, were sampled in this study. Their isolates were selected tested for antibacterial activity against pathogenic bacteria using the paper disc diffusion and Minimum Inhibitory Concentration methods and were molecularly identified based on the 16s RNA gene (27F-1492R). Twenty-one isolates were isolated from the 3 seaweed species: 11 from C. racemosa, 6 from P. minor, and 4 from H. opuntia. Further testing revealed potential isolates (C2a, C2c, C2d, and H2d) with antibacterial activity against P. acnes F2 ATCC 6919 and S. epidermidis FNCC-0048. Gene-based identification using 16s RNA (27F-1492R) demonstrated the occurrence of 4 bacterial species, namely Vibrionaceae bacterium PH25 (99.86 %), Vibrio alginolyticus strain GS MYPK1 (99.65 %), Salinivibrio costicola strain M318 (99.86 %), and V. alginolyticus strain 2014V-1011 (99.93 %). HIGHLIGHTS Bacteria associated with racemosa, P. minor, and H. opuntia can show strong antibacterial properties capable of mitigating the growth of P. acnes F2 ATCC 6919 and S. epidermidis FNCC-0048 Seaweed-associated bacteria and their antibacterial activity against skin disease agents. Gene-based identification using 16s RNA (27F-1492R) demonstrated the occurrence of 4 bacterial species, namely Vibrionaceae bacterium PH25 (99.86 %), Vibrio alginolyticus strain GS MYPK1 (99.65 %), Salinivibrio costicola strain M318 (99.86 %), and alginolyticus strain 2014V-1011 (99.93 %) The major bacteria species on the scalps of those suffering from dandruff, we believe these isolates may be useful for dandruff therapy GRAPHICAL ABSTRACT

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.

Detection of lukf-pv gene in Staphylococcus aureus isolated from pregnant women with Urinary tract infection

Staphylococcus aureus is a human pathogen as well as commensal bacteria. S. aureus has colonized around 30% of the human population. This study aimed to diagnose Staphylococcus aureus by molecular techniques, correlate the resistance against selected antimicrobial substances with the presence of the lukf-pv gene, and find the sequence of lukf-pv gene for the isolates obtained to investigate the mutations of those obtained isolates. This study included 60 patients diagnosed by the hospital with a urinary tract infection in Teaching Medical City Hospital, Baghdad, and Al-Yarmouk Teaching Hospital, between January 2021 and July 2021. The isolates were cultured on a blood agar overnight; then, isolates were diagnosed by VITEK as S. aureus. DNA has been isolated from all the included samples. A specific region of the 16SRNA gene has been amplified to diagnose S. aureus by molecular techniques. Then possession of the lukf-pv gene was tested by PCR, then amplified products were sequenced to detect the mutations within the lukf-pv gene. The finding appeared that blood group O+ has the highest rate of bacterial infection, the lowest is O- (1.7%), and the highest rate is shown within people not suffering from complicated diseases (65%). Of the 60 isolates, 60 (100%) were confirmed by 16sRNA gene amplification and were positive, among which 37 (61.6%) were lukf-pv positive. Results of the lukf-pv gene sequences showed around 501 bits score and 96% compatibility (ID: CP076105.1). The current study showed that antibiotics Cefoxitin, Benzylpenicillin, Oxacillin, Clindamycin, Fusidic acid, Rifampicin, Erythromycin, Vancomycin, and Teicoplanin had the highest resistance to antibiotics and as follow;100 %, 100 %, 40.54 %, 27.03 %, 27.03 %, 16.22 %, 13.51 %, and 10.81 %, respectively. Keywords: Staphylococcus aureus, 16sRNA and lukf-pv genes

Identification of Amylase-Producing Thermophilic Bacteria through 16sRNA Gene Analysis: MGH3 Strain

Thermostable amylase plays a role in the industrial sector because it is resistant to high temperatures, has high enzyme activity in various parameters and is economical in production costs. The thermostable amylase used in industry is stable and thermo activity. Bacteria that produce thermostable amylase can come from hot springs with temperatures above 80°C, such as Semurup hot springs, Kerinci, Jambi province, Indonesia. Semurup hot spring (Jambi) has a temperature of 82°C and a pH of 8.6. This causes variations in the content of organic, inorganic, and mineral compounds in the Semurup hot springs. The varied mineral content causes thermophilic bacteria to survive and the genetic diversity of thermophilic bacteria varies. This study aimed to molecularly identify thermostable amylase-producing thermophilic bacteria by analyzing the 16sRNA gene. Identification of bacteria was carried out by analyzing the 16S rRNA gene of thermophilic bacteria, such as DNA Isolation, DNA Amplification, 16S rRNA Gene Analysis, Alignment, and Phylogenetic Tree. There were 4 different bases between the bacterial isolates MGH3 and Bacillus licheniformis ATCC 14580, namely bases no. 87, 120, 967, and 1374. The difference of 4 bases in the two bacterial isolates already shows that the two isolates have a close kinship. So, most likely the MGH3 bacterial isolate is Bacillus licheniformis strain MGH3.

Qi-Long-Tian capsule alleviates pulmonary fibrosis development by modulating inflammatory response and gut microbiota.

Pulmonary fibrosis (PF) is a chronic, progressive, and fibrotic interstitial lung disease with a high mortality rate. Qi-Long-Tian (QLT) capsule is an herbal formula with great potential for antifibrotic effects, consisting of San Qi (Notoginseng Radix et Rhizoma), Di Long [Pheretima aspergillum (E. Perrier)], and Hong Jingtian (Rhodiolae Crenulatae Radix et Rhizoma), and has been used in clinical practice for many years. To explore the relationship between the effects of Qi-Long-Tian capsule and gut microbiota of PF mice, pulmonary fibrosis model were established by tracheal drip injection of bleomycin. Thirty-six mice were randomly divided into 6 groups: control group (control), model group (model), QLT capsule low dose group (QL), QLT capsule medium dose group (QM), QLT capsule high dose group (QH), and pirfenidone group (PFD). After 21days of treatment, after pulmonary function tests, the lung tissues, serums, and enterobacterial samples were collected for further analysis. HE staining and Masson's staining were used to detect changes as the main indicators of PF in each group, and the expression of hydroxyproline (HYP) related to collagen metabolism was detected by and alkaline hydrolysis method. qRT-PCR and ELISA were used to detect the mRNA and protein expressions of pro-inflammatory factors include interleukin 1β (IL-1β), interleukin 6 (IL-6), transforming growth factor β1 (TGF-β1), tumor necrosis factor α (TNF-α) in lung tissues and serums, and the inflammation-mediating factors include tight junction protein (ZO-1, Claudin, Occludin). ELISA was used to detect the protein expressions of secretory immunoglobulin A (sIgA), short-chain fatty acids (SCFAs), and lipopolysaccharide (LPS) in colonic tissues. 16sRNA gene sequencing was used to detect changes in the abundance and diversity of intestinal flora in the control, model, and QM groups, to search for differential genera, and analyze the correlation with inflammatory factors. QLT capsule effectively improved the status of pulmonary fibrosis and reduced HYP. In addition, QLT capsule significantly reduced the abnormal levels of pro-inflammatory factors, including IL-1β, IL-6, TNF-α, and TGF-β in lung tissue and serum, while improving the levels of pro-inflammatory related factors ZO-1, Claudin, Occludin, sIgA, SCFAs, and reducing LPS in the colon. The comparison between the alpha diversity and beta diversity in enterobacteria suggested that the composition of the gut flora in the control, model, and QLT capsule groups were different. QLT capsule significantly increased the relative abundance of Bacteroidia (which might limit the onset of inflammation) and decreased the relative abundance of Clostridia (which might promote inflammation). In addition, these two enterobacteria were closely associated with pro-inflammatory-related indicators and pro-inflammatory factors in PF. All these results suggest that QLT capsule intervenes in pulmonary fibrosis by regulating the differential genera of intestinal flora, increasing immunoglobulin secretion, repairing the intestinal mucosal barrier, reducing LPS entry into the blood, and decreasing inflammatory factor secretion in the serum, which in turn alleviates pulmonary inflammation. This study clarifies the therapeutic mechanism of QLT capsule in PF and provides a theoretical basis for it. It provides a theoretical basis for its further clinical application.