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Scientific Reports Nov 2021Extreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and...
Extreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and acid-producing bacteria (APB) are usually found in these places and can harm important processes due to increases in corrosion rates, biofouling and reservoir biosouring. Biocides such as glutaraldehyde, dibromo-nitrilopropionamide (DBNPA), tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and alkyl dimethyl benzyl ammonium chloride (ADBAC) are commonly used in oil fields to mitigate uncontrolled microbial growth. The aim of this work was to evaluate the differences among microbiome compositions and their resistance to standard biocides in four different Brazilian produced water samples, two from a Southeast Brazil offshore oil field and two from different Northeast Brazil onshore oil fields. Microbiome evaluations were carried out through 16S rRNA amplicon sequencing. To evaluate the biocidal resistance, the Minimum Inhibitory Concentration (MIC) of the standard biocides were analyzed using enriched consortia of SRB and APB from the produced water samples. The data showed important differences in terms of taxonomy but similar functional characterization, indicating the high diversity of the microbiomes. The APB and SRB consortia demonstrated varying resistance levels against the biocides. These results will help to customize biocidal treatments in oil fields.
Topics: Bacteria; Biodiversity; Biofilms; Biofouling; Corrosion; Culture Media; Desulfovibrio; Disinfectants; Environmental Microbiology; Geography; Glutaral; Microbial Sensitivity Tests; Microbiota; Oil and Gas Fields; RNA, Ribosomal, 16S; Steel; Sulfates; Water; Water Microbiology
PubMed: 34845279
DOI: 10.1038/s41598-021-02494-7 -
Frontiers in Microbiology 2023Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production.
INTRODUCTION
Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production.
METHODS
In the current study we examined whether the market weights of native chicken breeds were related to specific cecal bacteria, serum metabolites and inflammatory cytokines. We examined cecal bacterial taxa using 16S rDNA analysis along with untargeted serum metabolites and serum inflammatory cytokines.
RESULTS
We found that the cecal microbiota could explain 10.1% of the individual differences in chicken weights and identified key cecal bacterial genera that influenced this phenotype. The presence of spp. improved growth performance via bovinic acid metabolism. In contrast, and had a negative effect on growth by inducing expression of the inflammatory cytokine IL-6.
DISCUSSION
We were able to link specific bacterial genera with growth promotion in chickens and this study will allow further development of their use as probiotics in these animals.
PubMed: 36910194
DOI: 10.3389/fmicb.2023.1060458 -
Scientific Reports Nov 2021The association between the gut microbiota and the development of lupus is unclear. We investigated alterations in the gut microbiota after induction of lupus in a...
The association between the gut microbiota and the development of lupus is unclear. We investigated alterations in the gut microbiota after induction of lupus in a murine model using viral peptide of human cytomegalovirus (HCMV). Three treatment arms for the animals were prepared: intraperitoneal injection of HCMVpp65 peptide, adjuvant alone, and PBS injection. Feces were collected before and after lupus induction biweekly for 16S rRNA sequencing. HCMVpp65 peptide immunization induced lupus-like effects, with higher levels of anti-dsDNA antibodies, creatinine, proteinuria, and glomerular damage, compared with mice treated with nothing or adjuvant only. The Simpson diversity value was higher in mice injected with HCMVpp65 peptide, but there was no difference in ACE or Chao1 among the three groups. Statistical analysis of metagenomic profiles showed a higher abundance of various families (Saccharimonadaceae, Marinifiaceae, and Desulfovibrionaceae) and genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) in HCMVpp65 peptide-treated mice. Significant correlations between increased abundances of related genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) and HCMVpp65 peptide immunization-induced lupus-like effects were observed. This study provides insight into the changes in the gut microbiota after lupus onset in a murine model.
Topics: Animals; Bacteria; DNA, Bacterial; Disease Models, Animal; Feces; Gastrointestinal Microbiome; Lupus Erythematosus, Systemic; Metagenomics; Mice; Mice, Inbred NZB; RNA, Ribosomal, 16S
PubMed: 34824318
DOI: 10.1038/s41598-021-02422-9 -
MSphere Apr 2022Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ∼6,000 to 8,000 m. While the microbial communities in trench...
Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ∼6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, (Mariana Trench) and (Kermadec Trench), using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid and the continental shelf-dwelling snailfish . The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the and . These shared taxa indicate that symbiont lineages have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including , , and . These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats. Hadal trenches, characterized by high hydrostatic pressures and low temperatures, are one of the most extreme environments on our planet. By examining the microbiome of abyssal and hadal fishes, we provide insight into the diversity and distribution of host-associated life at great depth. Our findings show that there are similar microbial populations in fishes geographically separated by thousands of miles, reflecting strong selection for specific microbial lineages. Only a few psychropiezophilic taxa, which do not reflect the diversity of microbial life at great depth, have been successfully isolated in the laboratory. Our examination of deep-sea fish microbiomes shows that typical high-pressure culturing methodologies, which have largely remained unchanged since the pioneering work of Claude ZoBell in the 1950s, may simulate the chemical environment found in animal guts and helps explain why the same deep-sea genera are consistently isolated.
Topics: Adaptation, Physiological; Animals; Fishes; Gastrointestinal Microbiome; Microbiota; Perciformes; RNA, Ribosomal, 16S
PubMed: 35306867
DOI: 10.1128/msphere.00032-22 -
Microorganisms Apr 2021Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long...
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
PubMed: 33925267
DOI: 10.3390/microorganisms9050931 -
Molecular Cell Sep 2016Bacteria employ surveillance complexes guided by CRISPR (clustered, regularly interspaced, short palindromic repeats) RNAs (crRNAs) to target foreign nucleic acids for...
Bacteria employ surveillance complexes guided by CRISPR (clustered, regularly interspaced, short palindromic repeats) RNAs (crRNAs) to target foreign nucleic acids for destruction. Although most type I and type III CRISPR systems require four or more distinct proteins to form multi-subunit surveillance complexes, the type I-C systems use just three proteins to achieve crRNA maturation and double-stranded DNA target recognition. We show that each protein plays multiple functional and structural roles: Cas5c cleaves pre-crRNAs and recruits Cas7 to position the RNA guide for DNA binding and unwinding by Cas8c. Cryoelectron microscopy reconstructions of free and DNA-bound forms of the Cascade/I-C surveillance complex reveal conformational changes that enable R-loop formation with distinct positioning of each DNA strand. This streamlined type I-C system explains how CRISPR pathways can evolve compact structures that retain full functionality as RNA-guided DNA capture platforms.
Topics: Amino Acid Motifs; Bacterial Proteins; Binding Sites; CRISPR-Cas Systems; Cloning, Molecular; Cryoelectron Microscopy; DNA; Desulfovibrio vulgaris; Endonucleases; Escherichia coli; Gene Editing; Gene Expression; Kinetics; Models, Molecular; Nucleic Acid Conformation; Operon; Protein Binding; Protein Conformation, alpha-Helical; Protein Interaction Domains and Motifs; RNA, Bacterial; RNA, Guide, CRISPR-Cas Systems; Recombinant Proteins; Substrate Specificity
PubMed: 27588603
DOI: 10.1016/j.molcel.2016.07.027 -
Annals of Translational Medicine Jun 2022Yinzhihuang (YZH) oral liquid is a traditional Chinese medicine compound that has emerged as a promising therapeutic agent for non-alcoholic fatty liver disease (NAFLD)....
BACKGROUND
Yinzhihuang (YZH) oral liquid is a traditional Chinese medicine compound that has emerged as a promising therapeutic agent for non-alcoholic fatty liver disease (NAFLD). Here, we aimed to investigate the therapeutic effects of YZH on non-alcoholic steatohepatitis (NASH) and elucidate its underlying molecular mechanisms.
METHODS
Mice fed on a high-fat diet plus fructose/glucose drinking water (HFGD) were treated with YZH (30 mL/kg/d). The effects of YZH on mice with NASH were assessed through serological analysis and histological examination. Microbiota analysis based on 16S ribosomal ribonucleic acid (16S rRNA) and intestinal mucosal barrier function, serum inflammatory factors, hepatic macrophage infiltration, as well as hepatic toll-like receptor 4 (TLR4), myeloid differentiation primary response 88 (MyD88), nuclear factor kappa B (NFκB) pathway were carried out to explore the mechanism of YZH for treatment of NASH.
RESULTS
Results of the current study found that YZH effectively reduced body weight gain and adiposity and alleviated hepatocyte steatosis, hepatocyte ballooning, liver tissue lobular inflammation, as well as fibrosis. It also reduced the accumulation of triglycerides, cholesterol, and free fatty acids in the liver of the treated mice and normalized serum aspartate transaminase, alanine transaminase, and glucose levels as well as lipid metabolism. Meanwhile, YZH treatment significantly decreased the abundance of harmful bacteria, such as , and . Mechanistically, the present study found that YZH upregulated the expression of tight junction proteins, decreased serum lipopolysaccharide, interleukin 6, and tumor necrosis factor α levels, and increased interleukin 10 levels in serum. In the liver, YZH alleviated macrophage infiltration, especially that of pro-inflammatory macrophages. Moreover, it was found that YZH inhibited the canonical TLR4, MyD88, NFκB signaling pathway.
CONCLUSIONS
In conclusion, YZH may be a new agent for the prevention of NASH. Further, YZH alleviates gut microbiota dysbiosis, restores the intestinal mucosal barrier, and inhibits the canonical TLR4, MyD88, NFκB signaling pathway.
PubMed: 35813333
DOI: 10.21037/atm-21-4809 -
The FEBS Journal Feb 2020Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In...
Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.
Topics: Algal Proteins; Binding Sites; Chlamydomonas reinhardtii; Cloning, Molecular; Desulfovibrio; Escherichia coli; Evolution, Molecular; Gene Expression; Genetic Vectors; Iron-Sulfur Proteins; Microalgae; Models, Molecular; Multigene Family; Nitrates; Photosynthesis; Phylogeny; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Recombinant Proteins; Structural Homology, Protein
PubMed: 31361397
DOI: 10.1111/febs.15025 -
Mediators of Inflammation 2020This study was conducted to analyze plasma reproductive hormone and biochemical parameter changes, as well as fecal microbiota composition and metabolites in sows, at...
This study was conducted to analyze plasma reproductive hormone and biochemical parameter changes, as well as fecal microbiota composition and metabolites in sows, at different pregnancy and lactation stages, using Bama mini pig as an experimental animal model. We found that plasma prolactin (PRL), progesterone, follicle-stimulating hormone (FSH), and estrogen levels decreased from day 45 to day 105 of pregnancy. Plasma total protein and albumin levels were lower in pregnant sows, while glucose, urea nitrogen, total cholesterol, and high-density lipoprotein-cholesterol, as well as fecal acetate, butyrate, valerate, total short-chain fatty acids, skatole, and tyramine levels, were higher in lactating sows. Interestingly, the lactating sows showed lower -diversity and and relative abundances, while pregnant sows showed a higher relative abundance. Notably, the relative abundance was highest on day 7 of lactation. Spearman analysis showed a positive correlation between plasma triglyceride and cholinesterase levels and and relative abundances. Moreover, and relative abundances were also positively correlated with plasma FSH, LH, and E levels, as well as PRL and LH with Collectively, plasma reproductive hormones, biochemical parameters, and fecal microbiota composition and metabolite levels could alter along with pregnancy and lactation, which might contribute to the growth and development demands of fetuses and newborns.
Topics: Akkermansia; Albumins; Animals; Bacteroides; Blood Proteins; Clostridiales; Desulfovibrio; Estrogens; Feces; Female; Follicle Stimulating Hormone; Lactation; Luteinizing Hormone; Microbiota; Pregnancy; Pregnancy, Animal; Progesterone; Prolactin; Proteobacteria; Spirochaetales; Streptococcus; Swine; Swine, Miniature; Verrucomicrobia
PubMed: 33162832
DOI: 10.1155/2020/8829072 -
ACS Chemical Biology Jul 2022Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from...
Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S] clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S] centers range between -250 and -530 mV. Two distinct W signals were detected, W and W, which differ in only the -value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of W was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate W state of FdhAB.
Topics: Catalysis; Desulfovibrio; Desulfovibrio vulgaris; Dithionite; Electron Spin Resonance Spectroscopy; Formate Dehydrogenases; Formates; Metals; Oxidation-Reduction
PubMed: 35766974
DOI: 10.1021/acschembio.2c00336