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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 -
World Journal of Microbiology &... Feb 2021Diazotrophy in the Arctic environment is poorly understood compared to tropical and subtropical regions. Hence in this study, we report the abundance and diversity of...
Diazotrophy in the Arctic environment is poorly understood compared to tropical and subtropical regions. Hence in this study, we report the abundance and diversity of diazotrophs in Arctic fjord sediments and elucidate the role of environmental factors on the distribution of diazotrophs. The study was conducted during the boreal summer in the Kongsfjorden, an Arctic fjord situated in the western coast of Spitsbergen. The abundance of nifH gene was measured through quantitative real-time PCR and the diversity of diazotrophs was assessed by nifH targeted clone library and next generation sequence analysis. Results revealed that the abundance of nifH gene in the surface sediments ranged from 2.3 × 10 to 3.7 × 10 copies g. The δ-proteobacterial diazotrophs (71% of total sequence) were the dominant class observed in this study. Major genera retrieved from the sequence analysis were Desulfovibrionaceae (25% of total sequence), Desulfuromonadaceae (18% of total sequence) and Desulfobacteriaceae (10% of total sequence); these are important diazotrophic iron and sulfur-reducing bacterial clade in the Kongsfjorden sediments. The abundance of nifH gene showed a significant positive correlation TOC/TN ratio (r = 0.96, p ≤ 0.05) and total organic carbon (p ≤ 0.05) content in the fjord sediments. The higher TOC/TN ratio (4.24-14.5) indicated low nitrogen content organic matter in the fjord sediments through glacier runoff, which enhances the abundance and diversity of nitrogen fixing microorganisms.
Topics: Arctic Regions; Bacteria; Bacterial Proteins; Geologic Sediments; High-Throughput Nucleotide Sequencing; Ice Cover; Nitrogen Fixation; Oxidoreductases; Phylogeny; Sequence Analysis, DNA
PubMed: 33544264
DOI: 10.1007/s11274-020-02993-1 -
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 -
Food & Function Sep 2021This study aimed to elucidate the effect of punicic acid (PUA, cis9,trans11,cis13-18 : 3) on obesity and liver steatosis in mice induced by high-fat diet (HFD), and...
This study aimed to elucidate the effect of punicic acid (PUA, cis9,trans11,cis13-18 : 3) on obesity and liver steatosis in mice induced by high-fat diet (HFD), and to explore the possible mechanism. Mice were fed with either a HFD or a control diet for 8 weeks. Half of HFD-mice received daily supplementation of PUA. Supplementation with PUA ameliorated the liver steatosis and obesity in mice fed by HFD, as demonstrated by the decreased hepatic triglyceride accumulation, body weight gain and fat weight. A HFD increased the ratio of Firmicutes to Bacteroidetes, whereas supplementation with PUA effectively restored it. PUA supplementation counteracted the upregulation in family Desulfovibrionaceae and Helicobacteraceae, and the downregulation in Muribaculaceae and Bacteroidaceae induced by HFD. Correspondingly, the family of Desulfovibrionaceae was positively related, whereas Muribaculaceae was negatively related to the amount of epididymal and perirenal fat, and the level of liver triglyceride and total cholesterol. The family Helicobacteraceae was also positively related to the amount of epididymal and perirenal fat. Moreover, PUA supplementation counteracted the increase in the population of Anaerotruncus, Faecalibaculim, Mucispirillum, and the decrease in the population of Lactobacillus, Roseburia, Oscillibacter at the genus level induced by HFD. These results demonstrated that PUA can at least in part ameliorate obesity and liver steatosis in mice induced by HFD by regulating gut microbiota composition.
Topics: Animals; Bacteria; Diet, High-Fat; Fatty Liver; Gastrointestinal Microbiome; Humans; Linolenic Acids; Liver; Male; Mice; Mice, Inbred ICR; Obesity; Plant Oils; Pomegranate; Seeds
PubMed: 34241611
DOI: 10.1039/d1fo01152a -
Sleep Medicine Mar 2022Obstructive sleep apnea (OSA) is a highly prevalent sleep disorder, and has been associated with adverse metabolic outcomes. There is increasing evidence indicating the...
BACKGROUND AND OBJECTIVES
Obstructive sleep apnea (OSA) is a highly prevalent sleep disorder, and has been associated with adverse metabolic outcomes. There is increasing evidence indicating the important role of gut microbiota in OSA and its comorbidities, while the perturbation of intestinal microbial community elicited by OSA has yet to be well-characterized. Here, we investigated the effect of chronic intermittent hypoxia (IH), a hallmark feature of OSA, on gut microbiota in mice.
METHODS
Male C57BL/6 mice were exposed to a pattern of chronic IH or normoxic conditions for 6 weeks. Fecal samples were collected. The composition of microbiota was determined by 16S rRNA gene amplicon sequencing, and PICRUSt2 was performed to predict functional potential of gut microbiome.
RESULTS
In IH mice, accompanied with elevated systemic inflammation, gut microbiota were significantly altered, characterized by enriched Bacteroides, Desulfovibrionaceae and decreased Bifidobacterium. Bacterial operational taxonomic units (OTUs) were clustered into co-abundance groups (CAGs) as potential functional unit in response to IH exposure. One CAG including bacteria of Bacteroides acidifaciens and Desulfovibrionaceae was positively correlated with systemic inflammation in mice, while another CAG composed of bacteria in Muribaculaceae was negatively correlated. Prediction of metabolic pathways showed that, changes in microbiota from IH treatment mainly impacted on bile acid and fatty acid metabolism.
CONCLUSION
Our data demonstrated that dysbiosis of gut microbiome was associated with systemic inflammation and metabolism disorder, and emerges as a mediator for IH and its consequences. Targeting microbiota will be a promising approach to curtail metabolic risks of OSA clinically.
Topics: Animals; Bacteria; Dysbiosis; Gastrointestinal Microbiome; Humans; Hypoxia; Inflammation; Male; Mice; Mice, Inbred C57BL; RNA, Ribosomal, 16S; Sleep Apnea, Obstructive
PubMed: 35286865
DOI: 10.1016/j.sleep.2022.02.003 -
Archives of Microbiology Apr 2023Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate... (Review)
Review
Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.
Topics: Oil and Gas Fields; Oxidation-Reduction; Sulfates; Desulfovibrio; Bacteria; Sulfur
PubMed: 37010699
DOI: 10.1007/s00203-023-03520-0 -
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