Artificial insemination (AI) technology has greatly promoted the development of the chicken industry. Recently, AI technology has also begun to be used in the duck industry, but there are some ...problems. Numerous researchers have shown that microbes colonizing in semen can degrade semen quality, and AI can increase the harmful microbial load in hen's reproductive tract. Different from the degraded external genitalia of roosters, drakes have well-developed external genitalia, which may cause drake semen to be more susceptible to microbial contamination. However, information on the compositions, sources, and effects of semen microbes on semen quality remains unknown in drakes. In the current study, high-throughput sequencing technology was used to detect microbial communities in drake semen, environmental swabs, cloacal swabs, and the spermaduct after quantifying the semen quality of drakes to investigate the effects of microbes in the environment, cloaca, and spermaduct on semen microbiota and the relationships between semen microbes and semen quality. Taxonomic analysis showed that the microbes in the semen, environment, cloaca, and spermaduct samples were all classified into 4 phyla and 25 genera. Firmicutes and Proteobacteria were the dominant phyla. Phyllobacterium only existed in the environment, while Marinococcus did not exist in the cloaca. Of the 24 genera present in semen: Brachybacterium, Brochothrix, Chryseobacterium, Kocuria, Marinococcus, Micrococcus, Rothia, Salinicoccus, and Staphylococcus originated from the environment; Achromobacter, Aerococcus, Corynebacterium, Desemzia, Enterococcus, Jeotgalicoccus, Pseudomonas, Psychrobacter, and Turicibacter originated from the cloaca; and Agrobacterium, Carnobacterium, Chelativorans, Devosia, Halomonas, and Oceanicaulis originated from the spermaduct. In addition, K-means clustering analysis showed that semen samples could be divided into 2 clusters based on microbial compositions, and compared with cluster 1, the counts of Chelativorans (P < 0.05), Devosia (P < 0.01), Halomonas (P < 0.05), and Oceanicaulis (P < 0.05) were higher in cluster 2, while the sperm viability (P < 0.05), total sperm number (P < 0.01), and semen quality factor (SQF) (P < 0.01) were lower in cluster 2. Furthermore, functional prediction analysis of microbes showed that the activities of starch and sucrose metabolism, phosphotransferase system, ABC transporters, microbial metabolism in diverse environments, and quorum sensing pathways between cluster 1 and cluster 2 were significantly different (P < 0.05). Overall, environmental/cloacal microbes resulted in semen contamination, and microbes from the Chelativorans, Devosia, Halomonas, and Oceanicaulis genera may have negative effects on semen quality in drakes by affecting the activities of starch and sucrose metabolism, phosphotransferase system, ABC transporters, and quorum sensing pathways that are associated with carbohydrate metabolism. These data will provide a basis for developing strategies to prevent microbial contamination of drake semen.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Background: Streptomyces have the ability to produce bioactive metabolites such as antibacterial compounds. This study aimed to isolate and evaluate the production of antibacterial compounds from ...marine sediments by Streptomyces of eastern Gilan province. Materials and Methods: Marine sediments were collected and Streptomyces species were identified based on morphological, physiological, biochemical methods and molecular identification was used by 16SrRNA gene sequencing and phylogenetic analysis. Antimicrobial activity was evaluated against pathogenic microorganisms such as Micrococcus luteus PTCC 1408, Bacillus cereus PTCC 1154, Staphylococcus aureus PTCC 1189, Pseudomonas aeruginosa PTCC 1310, Salmonella typhi PTCC 1609 and Proteus mirabilis PTCC 1776 by using primary (Cross streak) and secondary (Well diffusion agar) methods were investigated. Results: The isolate SN7 was collected from marine sediments of eastern Gilan province, Iran and the results of 16SrRNA gene sequencing and phylogenetic analysis revealed that the isolate belonged to Streptomyces genus with the highest similarity (90.17%) to uncultured Streptomyces sp. and it can be introduced as a new species. This isolate showed significant antimicrobial activity against pathogenic microorganisms and P. aeruginosa was the most resistant microorganism against antimicrobial activity of this isolate. Conclusion: The results showed that the marine sediments of the eastern regions of Gilan province, Iran can be significant for producing antimicrobial compounds and these regions can be valuable for pharmaceutical application.
Increasing evidence has indicated dysbiosis of the gut microbiota in patients with pulmonary tuberculosis (PTB). However, the change in the intestinal microbiota varies between different studies. ...This systematic review was conducted to investigate the characteristics of the gut microbiota in PTB patients. The MBASE, MEDLINE, Web of Science, and Cochrane Library electronic databases were systematically searched, and the quality of the retrieved studies was evaluated using the Newcastle–Ottawa scale. A total of 12 studies were finally included in the systematic review. Compared with healthy controls, the index reflecting α-diversity including the richness and/or diversity index decreased in 6 studies, while β-diversity presented significant differences in PTB patients in 10 studies. Although the specific gut microbiota alterations were inconsistent, short-chain fatty acid-producing bacteria (including Lachnospiraceae, Ruminococcus, Blautia, Dorea, and Faecalibacterium), bacteria associated with an inflammatory state (e.g., Prevotellaceae and Prevotella), and beneficial bacteria (e.g., Bifidobacteriaceae and Bifidobacterium) were commonly noted. Our systematic review identifies key evidence for gut microbiota alterations in PTB patients, in comparison with healthy controls; however, no consistent conclusion could be drawn, due to the inconsistent results and heterogeneous methodologies of the enrolled studies. Therefore, more well-designed research with standard methodologies and large sample sizes is required.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The aim of this study is to provide a reference frame to allow the comparison and interpretation of currently published studies on 16S ribosomal ribonucleic acid amplicon sequencing of ocular ...microbiome samples using different DNA extraction protocols. Alongside, the quantitative and qualitative yield and the reproducibility of different protocols has been assessed.
Both eyes of 7 eligible volunteers were sampled. Five commercially available DNA extraction protocols were selected based on previous publications in the field of the ocular surface microbiome and 2 host DNA depletion protocols were added based on their reported effective host DNA depletion without significant reduction in bacterial DNA concentration. The V3-V4 region of the 16S rRNA gene was targeted using Illumina MiSeq sequencing. The DADA2 pipeline in R was used to perform the bio-informatic processing and taxonomical assignment was done using the SILVA v132 database. The Vegdist function was used to calculate Bray-Curtis distances and the Galaxy web application was used to identify potential metagenomic biomarkers
linear discriminant analysis Effect Size (LEfSe). The R package Decontam was applied to control for potential contaminants.
Samples analysed with PowerSoil, RNeasy and NucleoSpin had the highest DNA yield. The host DNA depletion kits showed a very low microbial DNA yield; and these samples were pooled per kit before sequencing. Despite pooling, 1 of both failed to construct a library.Looking at the beta-diversity, clear microbial compositional differences - dependent on the extraction protocol used - were observed and remained present after decontamination. Eighteen genera were consistently retrieved from the ocular surface of every volunteer by all non-pooled extraction kits and a comprehensive list of differentially abundant bacteria per extraction method was generated using LefSe analysis.
High-quality papers have been published in the field of the ocular surface microbiome but consensus on the importance of the extraction protocol used are lacking. Potential contaminants and discriminative genera per extraction protocol used, were introduced and a reference frame was built to facilitate both the interpretation of currently published papers and to ease future choice - making based on the research question at hand.
A Gram-stain-negative, aerobic, gliding, rod-shaped (0.2-0.5×1.0-13.0 µm) and yellow-pigmented bacterium, designated PLHSN227
, was isolated from seawater collected near the coast of Yantai, PR ...China. PLHSN227
was found to grow at 15-37 °C (optimum, 28-30 °C) and pH 6.0-8.5 (optimum, 6.5-7.5) in the presence of 2-14 % (w/v) NaCl (optimum, 5.0 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that PLHSN227
represented a member of the family
and exhibited the highest sequence similarity (94.6 %) to the type strain
NBRC 100249
. The chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included C
ω8
, iso-C
, anteiso-C
, C
and summed feature 8 (C
ω7
and/or C
ω6
). The major polar lipids included phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content of PLHSN227
was 35.6 mol%. PLHSN227
showed the highest average amino acid identity value of 67.2 %, the average nucleotide identity value of 75.6 and 14.5 % digital DNA-DNA hybridization identity with
DSM 15361
. According to the phylogenetic data, PLHSN227
formed a distinct clade in the phylogenetic tree. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is considered that PLHSN227
represents a novel genus within the family
, for which the name
gen. nov., sp. nov. is proposed. The type strain is PLHSN227
(=KCTC 72159
=MCCC 1H00371
).
Background
IL‐13 is considered an archetypal T2 cytokine central to the clinical disease expression of asthma. The IL‐13 response genes, which are upregulated in central airway bronchial epithelial ...of asthma patients, can be normalized by high‐dose inhaled steroid therapy in severe asthma. However, this is not the case within the peripheral airways. We have sought to further understand IL‐13 in the peripheral airways in severe asthma through bronchoalveolar analysis.
Methods
Bronchoalveolar lavage samples were collected from 203 asthmatic and healthy volunteers, including 78 with severe asthma. Inflammatory mediators were measured using a multiple cytokine immunoassay platform. This analysis was replicated in a further 59 volunteers, in whom 16S rRNA analysis of BAL samples was undertaken by terminal restriction fragment length polymorphism.
Results
Severe asthma patients with high BAL IL‐13, despite treatment with high‐dose inhaled corticosteroids, had more severe lung function and significantly higher BAL neutrophil percentages, but not BAL eosinophils than those with normal BAL‐13 concentrations. This finding was replicated in the second cohort, which further associated BAL IL‐13 and neutrophilia with a greater abundance of potentially pathogenic bacteria in the peripheral airways.
Conclusion
Our findings demonstrate a steroid unresponsive source of IL‐13 that is associated with BAL neutrophilia and bacterial dysbiosis in severe asthma. Our findings highlight the biological complexity of severe asthma and the importance of a greater understanding of the innate and adaptive immune responses in the peripheral airways in this disease.
In this study, we stratified biologic naïve severe asthma patients treated with high‐dose inhaled corticosteroid therapy by their bronchoalveolar lavage IL‐13. Patients with high bronchoalveolar lavage IL‐13, despite steroid therapy, have a higher percentage of bronchoalveolar lavage neutrophils. We replicated these findings in a second smaller cohort, which also associated high bronchoalveolar lavage IL‐13 with bacterial dysbiosis.
Abbreviations: BAL, bronchoalveolar lavage; ICS, inhaled corticosteroids; OCS, oral corticosteroids.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background: Mucuna (Mucuna pruriens L.) is an annual herbaceous climber, grown as a medicinal, green manure, cover and smothering crop. The mucuna seeds contains L-DOPA (L-3, 4 dihydroxy ...phenylalanine), a non-protein amino acid, extensively used for Parkinson and hypertensive drug. Injudicious application of nitrogenous fertilizers leads to deterioration of soil quality which results into loss of crop yield and quality. The application of microbial inoculant containing efficient native rhizobia enhances the nodular properties, N2-fixation and soil quality. Therefore, Rhizobium strain associated with mucuna was isolated, biochemically characterized and identified. The 16SrRNA sequencing revealed that Sinnorhizobium mililoti, a gram negative symbiotic nitrogen fixing bacteria is present in root nodules of mucuna. Methods: Root nodules were extracted from mucuna grown at ICAR- Krishi Vigyan Kendra, Doddaballapura Taluk, Bengaluru Rural District, Karnataka, then cultured, screened and characterized in the laboratory. The 16SrRNA sequencing and phylogenetic analysis was done to identify the native rhizobial strain. Result: Identification of native root nodulating bacteria through 16SrRNA sequencing concluded that Sinnorhizobium mililoti strain associated with the root nodules of Mucuna (Mucuna pruriens L.).
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
This study investigated the effects of dietary supplements, citrus (CTS) and cucumber (CMB), on the jejunum and cecum microbiota of 14- and 28-days old broiler chickens to evaluate their impact on ...the gut health and assess their role as alternatives to antibiotic growth promoters (ABGPs). 16SrRNA gene sequencing revealed the overall bacterial microbiota composition was significantly affected by the gut site (p?<?0.001) but not by either of the dietary supplements, CTS and CMB, at both 14 and 28 days of age. However, as a result of Linear discriminant analysis (LDA) effect size (LEfSE), CTS dietary supplements significantly increased the counts of Lactobacillus (p?<?0.01) and decreased the counts of Enterococcus (p?<?0.01) and Clostridium (p?<?0.05) in the jejunum, whereas the counts of Blautia were increased (p?<?0.01) and Enterococcus were decreased (p?<?0.05) in the cecum at both ages. Only minor CMB effects were identified in the cecum and non in the jejunum. The use of CTS dietary supplements has been shown to be associated to the reduction of potentially pathogenic bacteria (Enterococcus and Clostridium) and to the growth of beneficial bacteria (Lactobacillus and Blautia) which are known to have positive effects on chicken health in terms of nutrients absorption, stimulation and production of short chain fatty acids (SCFAs). Therefore, this study suggests that the use of a CTS supplemented diet could promote gut health while no clear advantages have been identified with the use of CMB as a dietary supplement.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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