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The ISME Journal Apr 2021Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often...
Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.
Topics: Benzoates; Ferric Compounds; Geologic Sediments; In Situ Hybridization, Fluorescence; Iron; Oxidation-Reduction; Oxides
PubMed: 33154547
DOI: 10.1038/s41396-020-00824-7 -
Microbiological Research May 2022Malaria, caused by Plasmodium, is a global life-threatening infectious disease. However, the dynamic interactions between intestinal microbiota and host immunity during...
Malaria, caused by Plasmodium, is a global life-threatening infectious disease. However, the dynamic interactions between intestinal microbiota and host immunity during the infections are still unclear. Here, we investigated the change of intestinal microbiome and transcriptome during Plasmodium yoelii infection in mice. The mice were infected with P. yoelii through the intraperitoneal injection. The intestinal contents and tissues were collected at different time points along with the malaria procession and they were subjected to the microbiome and transcriptome sequencing and analysis respectively. The dynamic landscape of parasitemia-dependent intestinal microbiota and related host immunity were identified: (1) The diversity and composition of the intestinal microbiota represented a significant correlation with the Plasmodium infection; (2) Up-regulated genes from the intestinal transcriptome were mainly enriched in immune cell differentiation pathways, especially, naive CD4+ T cell differentiation to Th1/2 cells in the early immune response and Th17 cells in the later immune stage, T cell receptor (TCR) and B cell receptor (BCR) activation in the whole host immunity; (3) Host immune cells presented parasitemia phase-specific characteristics against P. yoelii infection; (4) There were significant associations between the parasitemia phase-specific microbiotas and the host immune response. Th1 cell differentiation was positively correlated with genera Moryella and specie Erysipelotrichaceae bacterium canine oral taxon 255, while negatively correlated with genera Ruminiclostridium. Th17 cell differentiation was related to the colonization of family Peptococcaceae, genera Lachnospiraceae FCS020 group, and specie Eubacterium plexicaudatum ASF492 and the reduction of family Bacteroidales BS11 gut group, genera Sutterella, and specie Parabacteroides distasonis str. 3776 D15 I. BCRs and TCRs were highly related with the family Bacteroidales BS11 gut group, genera Moryella, and specie Erysipelotrichaceae bacterium canine oral taxon 255, but negatively related with the genera Ruminiclostridium. Our results indicated a remarkable dynamic landscape and correlation of the parasitemia-dependent shifting of intestinal microbiota and immunity, suggesting the essential roles of intestinal microbiome on the modulation of host immunity against Plasmodium infection.
Topics: Animals; Dogs; Gastrointestinal Microbiome; Malaria; Mice; Parasitemia; Plasmodium yoelii; Transcriptome
PubMed: 35220138
DOI: 10.1016/j.micres.2022.126994 -
Scientific Reports Jan 2024A growing number of studies have implicated that gut microbiota abundance is associated with myasthenia gravis (MG). However, the causal relationship underlying the...
A growing number of studies have implicated that gut microbiota abundance is associated with myasthenia gravis (MG). However, the causal relationship underlying the associations is still unclear. Here, we aim to investigate the causal effect of gut microbiota on MG using Mendelian randomization (MR) method. Publicly available Genome-wide association study (GWAS) summary-level data for gut microbiota and for MG were extracted. Inverse variance weighted was used as the main method to analyze causality. The robustness of the results was validated with sensitivity analyses. Our results indicated that genetically predicted increased phylum Lentisphaerae (OR = 1.319, p = 0.026), class Lentisphaerae (OR = 1.306, p = 0.044), order Victivallales (OR = 1.306, p = 0.044), order Mollicutes (OR = 1.424, p = 0.041), and genus Faecalibacterium (OR = 1.763, p = 0.002) were potentially associated with a higher risk of MG; while phylum Actinobacteria (OR = 0.602, p = 0.0124), class Gammaproteobacteria (OR = 0.587, p = 0.036), family Defluviitaleaceae (OR = 0.695, p = 0.047), family Peptococcaceae (OR = 0.698, p = 0.029), and family Family XIII (OR = 0.614, p = 0.017) were related to a lower risk of MG. The present study provides genetic evidence for the causal associations between gut microbiota and MG, thus suggesting novel insights into the gut microbiota-neuromuscular junction axis in the pathogenesis of MG.
Topics: Humans; Gastrointestinal Microbiome; Genome-Wide Association Study; Mendelian Randomization Analysis; Myasthenia Gravis; Neuromuscular Junction
PubMed: 38291090
DOI: 10.1038/s41598-024-52469-7 -
FEMS Microbiology Ecology Jan 2017The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and...
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.
Topics: Anaerobiosis; Benzene; Benzene Derivatives; Biodegradation, Environmental; Deltaproteobacteria; Ecosystem; Groundwater; Hydrocarbons; Toluene; Water Pollutants, Chemical; Xylenes
PubMed: 27810873
DOI: 10.1093/femsec/fiw220 -
Animals : An Open Access Journal From... Oct 2021Epilepsy is one of the most common neurological disorders in humans and dogs. The structure and composition of gut microbiome associated to this disorder has not yet...
Epilepsy is one of the most common neurological disorders in humans and dogs. The structure and composition of gut microbiome associated to this disorder has not yet been analyzed in depth but there is evidence that suggests a possible influence of gut bacteria in controlling seizures. The aim of this study was to investigate the changes in gut microbiota associated to canine idiopathic epilepsy (IE) and the possible influence of antiepileptic drugs (AEDs) on the modulation of this microbiota. Faecal microbiota composition was analyzed using sequencing of bacterial 16S rRNA gene in a group of healthy controls ( = 12) and a group of epileptic dogs both before ( = 10) and after a 30-day single treatment with phenobarbital or imepitoin ( = 9). Epileptic dogs showed significantly reduced abundance of GABA (, and ) and SCFAs-producing bacteria ( and ) as well as bacteria associated with reduced risk for brain disease () than control dogs. The administration of AEDs during 30 days did not modify the gut microbiota composition. These results are expected to contribute to the understanding of canine idiopathic epilepsy and open up the possibility of studying new therapeutic approaches for this disorder, including probiotic intervention to restore gut microbiota in epileptic individuals.
PubMed: 34827852
DOI: 10.3390/ani11113121 -
Frontiers in Microbiology 2021Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial...
Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH and H), (ii) CO sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L and a phosphate content of 0.02mg.L. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, , , and ), fermentative (e.g., SCADC1_2_3, Anaerolineae lineage and ), and homoacetogenic bacteria (" Acetothermia") with a few archaeal representatives (e.g., , , and members of the Bathyarcheia class), suggesting a role of H in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
PubMed: 34721313
DOI: 10.3389/fmicb.2021.688929 -
ISME Communications Jan 2024Nitrous oxide (NO), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by NO reductase (NosZ). Bacteria...
Nitrous oxide (NO), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by NO reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH NO reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) NO assessed NO reduction at pH 4.5 and 7.3. All microcosms consumed NO, with lag times of up to 7 months observed in microcosms with 2 mM NO. Comparative metagenome analysis revealed that dominated in circumneutral microcosms under both NO feeding regimes. At pH 4.5, dominated in high-NO, and in low-NO microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the NO-reducing microcosms harbored operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type and lacking nitrite reductase genes (/). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored NO-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that genes commonly occur, suggesting broad distribution of NO reduction potential in acidic soils.
PubMed: 38808123
DOI: 10.1093/ismeco/ycae070 -
Nature Communications Jan 2018Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and...
Methanol is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17, isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.
Topics: Alcohol Dehydrogenase; Bacterial Proteins; Cobalt; Culture Media; Desulfotomaculum; Gene Expression; Gene Expression Profiling; Hydrolysis; Metabolic Networks and Pathways; Methanol; Methyltransferases; Oxidation-Reduction; Phylogeny; Proteomics; Vitamin B 12
PubMed: 29339722
DOI: 10.1038/s41467-017-02518-9 -
Frontiers in Microbiology 2021Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that...
Intestinal infections are a major cause of morbidity and mortality in humans and agricultural animals, especially newborns and weaned animals. Preventive treatments that help weaned animals maintain homeostasis and balance the hindgut microbial populations are desirable. The present study aimed to explore the impact of bacitracin methylene disalicylate (BMD) on the intestinal health by analyzing the intestinal environment, morphology, expression of peptidoglycan recognition proteins (PGRPs), and flora of weaned rabbits. A total of 300 New Zealand weaned rabbits were randomly divided into the following five treatment groups for a 35-day feed trial: control group (basal diet), bacitracin zinc (BZ) group (50 mg/kg BZ), BMDa group (100 mg/kg BMD), BMDb group (50 mg/kg BMD), and BMDc group (rabbits fed a basal diet supplemented with 25 mg/kg BMD). In each treatment group, 28 rabbits were slaughtered for experimental analysis. The results showed that the supplementation of BMD increased the environmental acidity of the cecum of the weaned rabbits and reduced the ammonia-nitrogen concentration, which was beneficial to the survival of useful bacteria in the intestine. The morphology analysis of the duodenum using hematoxylin and eosin staining revealed that the villus length, villus/crypt ratio, and intestinal wall thickness increased in the BMD group, thereby improving the structure of the duodenum and the absorption capacity of the small intestine. Moreover, real-time polymerase chain reaction test showed that PGRPs (especially PGLYRP-1 and PGLYRP-2) in the intestinal had an antagonistic effect with BMD in the process of inhibiting pathogenic bacteria, resulting in their decreased expression ( < 0.05). Furthermore, through 16S rRNA sequencing in the cecal content, the abundance of the predominant phyla in the BMDa and BZ groups was found to be the closest. The abundance of the genera , ), (), , (), , , and increased in the BMDa and BZ groups ( < 0.05). The relative abundance of , , and significantly increased only in the BMDa group ( < 0.05). Conclusively, BMD, as well as microbes, improved the intestinal environment and structure to maintain the intestinal health of weaned rabbits.
PubMed: 34248860
DOI: 10.3389/fmicb.2021.579006 -
Biomedicine & Pharmacotherapy =... Dec 2021The consumption of a high-fat diet can cause metabolic syndrome and induces host gut microbial dysbiosis and non-alcoholic fatty liver disease (NAFLD). We evaluated the...
The consumption of a high-fat diet can cause metabolic syndrome and induces host gut microbial dysbiosis and non-alcoholic fatty liver disease (NAFLD). We evaluated the effect of polyphenol-rich jaboticaba peel and seed powder (JPSP) on the gut microbial community composition and liver health in a mouse model of NAFLD. Three-month-old C57BL/6 J male mice, received either a control (C, 10% of lipids as energy, n = 16) or high-fat (HF, 50% of lipids as energy, n = 64) diet for nine weeks. The HF mice were randomly subdivided into four groups (n = 16 in each group), three of which (HF-J5, HF-J10, and HF-J15) were supplemented with dietary JPSP for four weeks (5%, 10%, and 15%, respectively). In addition to attenuating weight gain, JPSP consumption improved dyslipidemia and insulin resistance. In a dose-dependent manner, JPSP consumption ameliorated the expression of hepatic lipogenesis genes (AMPK, SREBP-1, HGMCoA, and ABCG8). The effects on the microbial community structure were determined in all JPSP-supplemented groups; however, the HF-J10 and HF-J15 diets led to a drastic depletion in the species of numerous bacterial families (Bifidobacteriaceae, Mogibacteriaceae, Christensenellaceae, Clostridiaceae, Dehalobacteriaceae, Peptococcaceae, Peptostreptococcaceae, and Ruminococcaceae) compared to the HF diet, some of which represented a reversal of increases associated with HF. The Lachnospiraceae and Enterobacteriaceae families and the Parabacteroides, Sutterella, Allobaculum, and Akkermansia genera were enriched more in the HF-J10 and HF-J15 groups than in the HF group. In conclusion, JPSP consumption improved obesity-related metabolic profiles and had a strong impact on the microbial community structure, thereby reversing NAFLD and decreasing its severity.
Topics: Animals; Bacteria; Blood Glucose; Diet, High-Fat; Disease Models, Animal; Dysbiosis; Gastrointestinal Microbiome; Inflammation Mediators; Intestines; Lipid Metabolism; Liver; Male; Mice, Inbred C57BL; Myrtaceae; Non-alcoholic Fatty Liver Disease; Plant Extracts; Powders; Prebiotics; Mice
PubMed: 34634561
DOI: 10.1016/j.biopha.2021.112314