Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil
Wenwen DengAnyun ZhangShujuan ChenXueping HeLei JinXiumei YuShengzhi YangBei LiLiangqian FanLin JiXin PanLikou Zou
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Chicken manure
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clone (Java method)
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Currently, there is a search for substances that would be very well tolerated by an organism and which could contribute to the activation of the growth of Bacteroidetes and Actinobacteria strains, with simultaneous inhibition of the growth of Firmicutes. High expectations in this regard are raised with the use of fiber preparations from starch - resistant corn dextrins, branched dextrins, resistant maltodextrins and soluble corn fiber. In this paper, the influence of fiber preparations made from corn starch was evaluated on growth and activity of Bacteroidetes, Actinobacteria and Firmicutes strains isolated from obese children. It was demonstrated that in the stool of obese children Firmicutes strains predominate, while Bacteroidetes and Actinobacteria strains were in the minority. A supplementation of fecal culture with fiber preparations did not cause any significant changes in the number of strains of Bacteroidetes and Firmicutes. Addition of fiber preparations to the fecal samples of obese children increased the amount of short-chain fatty acids, especially acetic (p < 0.01), propionic, butyric (p = 0.05) and lactic acid (p < 0.01).
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Pyrosequencing
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Bacteria found in operating rooms (ORs) might be clinically relevant since they could pose a threat to patients. In addition, C-sections operations are performed in ORs that provide the first environment and bacterial exposure to the sterile newborns that are extracted directly from the uterus to the OR air. Considering that at least one third of neonates in the US are born via C-section delivery (and more than 50% of all deliveries in some countries), understanding the distribution of bacterial diversity in ORs is critical to better understanding the contribution of the OR microbiota to C-section- associated inflammatory diseases. Here, we mapped the bacteria contained in an OR after a procedure was performed; we sampled grids of 60x60 cm across walls and wall-adjacent floors and sequenced the V4 region of 16S rRNA gene from 260 samples. The results indicate that bacterial communities changed significantly (ANOSIM, p-value < 0.001) with wall height, with an associated reduction of alpha diversity (t-test, p-value <0.05). OR walls contained high proportions of Proteobacteria, Firmicutes, and Actinobacteria, with Proteobacteria and Bacteroidetes being the highest in floors and lowest in the highest wall sites. Members of Firmicutes, Deinococcus-thermus, and Actinobacteria increased with wall height. Source-track analysis estimate that human skin is the major source contributing to bacterial composition in the OR walls, with an increase of bacteria related to human feces in the lowest walls and airborne bacteria in the highest wall sites. The results show that bacterial exposure in ORs varies spatially, and evidence exposure of C-section born neonates to human bacteria that remain on the floors and walls, possibly accumulated from patients, health, and cleaning staff.
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Thermus
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Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.
Fusobacteria
Bacterial phyla
Planctomycetes
Verrucomicrobia
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Проведены биохимический анализ крови и исследование химического состава образцов крови 163 пациентов в возрасте 45–90 лет с сахарным диабетом 2-го типа и дислипидемиями. В крови определяли концентрации жирных кислот, альдегидов, стиролов, имеющих микробное происхождение, а также уровни глюкозы, триглицеридов, холестерина, липидов низкой и высокой плотности. Химический состав крови определяли методом газовой хромато-масс-спектрометрии. По концентрациям жирных кислот, альдегидов, стиролов рассчитывали суммарную молярную концентрацию малых молекул микробного происхождения (Small molecules originating from microbes, SMOM), концентрацию октадеценового альдегида (18a), суммарную концентрацию гидроксикислот, производных гидроксильного остатка липида А, бактериального эндотоксина (3OH-FA) и сгруппированные суммарные концентрации химических соединений микробного происхождения, определяющих представительство основных четырех филотипов микробиома человека: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes . В результате исследования были получены данные об увеличении суммарной концентрации химических соединений, концентрации октадеценового альдегида и концентрации 3OH-FA у пациентов при нарушении углеводного обмена по типу сахарного диабета 2-го типа. Снижение представленности Bacteroidetes отмечали при нарушении углеводного обмена и снижение представленности Proteobacteria и Firmicute s – при нарушении углеводного и липидного обменов, а также увеличение представленности Actinobacteria – при нарушении липидного обмена, в том числе сочетанного с нарушением углеводного обмена. У пациентов с сахарным диабетом 2-го типа и в контрольной группе отмечена обратная корреляция между представленностью Firmicutes и уровнем глюкозы в крови. В группе пациентов с сахарным диабетом 2-го типа отмечена прямая корреляция представленности Bacteroidetes и уровня триглицеридов в крови. При нарушениях липидного обмена не выявлено ни статистически значимых изменений концентраций микробных маркеров в крови пациентов, ни статистически значимых корреляционных связей биохимических параметров крови и представленности филотипов микробиома.
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[Objective] Investigating the diversity of the cultivable bacteria in marine sediment environments. [Methods] Twenty sediment samples collected from South China Sea were used for bacterial diversity research by using the culture dependent method and 16S rRNA gene sequencing. [Results] Total of 200 strains were obtained, which belong to 47 genera and 99 species and spread in four phyla: Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The predominant group is phylum Firmicutes, in which genus Bacillus takes a great proportion of 55.6%. A few strains in phyla Actinobacteria and Bacteroidetes were also obtained. Eight potential new species and 3 potential new genera were discovered in phyla Firmicutes and Actinobacteria. [Conclusion] The preliminary study indicates that genus Bacillus is the dominant group in sediment environments of South China Sea and bacterial diversity showed a decreasing trend with the increase of sampling depth. Sampling depth maybe is one of the important factors to influence the distribution of bacteria. Diversity of bacteria and novel bio-resources in the sediment environments are very abundant and need to be further researched. Isolating methods and isolation media are the crucial factors to recover the microorganisms inhabiting the sediment environments.
Bacterial phyla
Bacillus (shape)
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