Enterobacterales from dairy cattle manure digesters
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ABSTRACT:
PROVIDER: PRJNA833106 | ENA |
REPOSITORIES: ENA
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Project description:Proteus mirabilis is an opportunistic pathogen associated with a variety of human infections, including urinary tract infections. The prevalence of P. mirabilis in foods of animal origin and in the manure by-products created in animal production is not well documented. Further, the prevalence and persistence of extended-spectrum cephalosporin (ESC) resistant P. mirabilis is largely unknown. In this study, we characterized ESC-resistant P. mirabilis recovered from various stages of dairy manure anaerobic digestion. Isolates were screened by PCR for blaCTX-M, blaCMY and blaSHV, and antimicrobial susceptibility testing was performed. Fifty-six P. mirabilis carrying CTX-M were sequenced with short and long read sequencing technologies, and the assembled chromosomes and plasmids were compared. ESC-resistant Proteus was found in four of the six manure digesters, an indication that not all digesters were colonized with resistant strains. Both CTX-M-1 and CTX-M-15 plasmids were found in P. mirabilis isolates. Transfer of plasmid DNA by conjugation was also explored, with ESC-resistance plasmids able to transfer to Escherichia coli at high frequency. We concluded that P. mirabilis can harbour and transfer ESC-resistance genes and plasmids, and may be an overlooked reservoir of antimicrobial resistance.
| S-EPMC10414651 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE35746: Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [tiling arrays] GSE35821: Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq] Refer to individual Series
2012-07-29 | E-GEOD-35822 | biostudies-arrayexpress
Project description:Dynamics of faecal shedding of Extended Spectrum beta-Lactamase or AmpC-producing Escherichia coli on dairy farms
| PRJEB30024 | ENA
Project description:BACKGROUND:House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae. RESULTS:Bacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities. CONCLUSIONS:House fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.
| S-EPMC8672618 | biostudies-literature
Project description:Although there are a variety of commercially available biological and chemical treatments for removal of hydrogen sulfide (H2S) from biogas, managing biogas H2S remains a significant challenge for agricultural digesters where labor and operational funds are very limited compared to municipal and industrial digesters. The objectives of this study were to evaluate headspace aeration for reducing H2S levels in low cost plug flow digesters and to characterize the relationship between the liquid surface area and H2S oxidation rates. Experiments with replicate field scale plug flow digesters showed that H2S levels decreased from 3500 ppmv to <100 ppmv when headspace oxygen levels were 0.5 to 1%. Methane production was not affected by aeration rates that resulted in headspace oxygen levels of up to 1%. Pilot scale experiments using 65 to 104 L desulfurization units showed that H2S oxidation rates increased with increases in liquid surface area. These results support the hypothesis that H2S oxidation rates are limited, in part, by the surface area available for oxygen transfer, and can be increased by growth of biofilms containing H2S oxidizing bacteria. Maximum removal rates corresponded to 40 to 100 g S m-2 d-1 of liquid surface area at biogas retention times of 30 to 40 min.
| S-EPMC5627928 | biostudies-literature
Project description:<p>Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease. </p>
| phs001352 | dbGaP
Project description:This paper describes the role of ambient pressure in self-heating torrefaction of livestock manure. We explored the initiating temperatures required to cause self-heating of wet dairy cattle manure at different ambient pressures (0.1, 0.4, 0.7, and 1.0 MPa). Then, we conducted proximate, elemental, and calorific analyses of biochar torrefied at 210, 250, and 290°C. The results showed that self-heating was induced at 155°C or higher for 0.1 MPa and at 115°C or lower for 0.4 MPa or higher. The decrease of the initiating temperature at elevated pressure was due not only to more oxygen, but also to the retention of moisture that can promote chemical oxidation of manure. Biochar yields decreased with increasing torrefaction temperature and pressure, and the yield difference at 0.1 and 1.0 MPa was more substantial at lower temperatures: a 29.8, 16.4, and 9.4% difference at 210, 250, and 290°C, respectively. Proximate and elemental analyses showed that elevated pressure promotes devolatilization, deoxygenation, and coalification compared to atmospheric pressure; its impact, however, was less at higher temperatures as the torrefaction temperature became more dominant. Calorific analysis revealed that elevated pressure can increase the higher heating value (HHV) on a dry and ash-free basis at 210°C because of the increase in carbon content, but its impact is limited at 250 and 290°C. Meanwhile, the HHV on a dry basis exhibited the opposite trend due primarily to an enlargement of ash content. The present study revealed that ambient pressure considerably affects the initiating temperature of self-heating and the chemical properties of biochar at a low torrefaction temperature.
| S-EPMC7259747 | biostudies-literature
Project description:Fosfomycin resistant Escherichia coli and Citrobacter freundii
| PRJNA900397 | ENA
Project description:The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals.
| S-EPMC4022807 | biostudies-literature