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MicrobiologyOpen Mar 2019Recent studies have shown that interspecies electron transfer between chemoheterotrophic bacteria and methanogenic archaea can be mediated by electric currents flowing...
Recent studies have shown that interspecies electron transfer between chemoheterotrophic bacteria and methanogenic archaea can be mediated by electric currents flowing through conductive iron oxides, a process termed electric syntrophy. In this study, we conducted enrichment experiments with methanogenic microbial communities from rice paddy soil in the presence of ferrihydrite and/or sulfate to determine whether electric syntrophy could be enabled by biogenic iron sulfides. Although supplementation with either ferrihydrite or sulfate alone suppressed methanogenesis, supplementation with both ferrihydrite and sulfate enhanced methanogenesis. In the presence of sulfate, ferrihydrite was transformed into black precipitates consisting mainly of poorly crystalline iron sulfides. Microbial community analysis revealed that a methanogenic archaeon and iron- and sulfate-reducing bacteria (Methanosarcina, Geobacter, and Desulfotomaculum, respectively) predominated in the enrichment culture supplemented with both ferrihydrite and sulfate. Addition of an inhibitor specific for methanogenic archaea decreased the abundance of Geobacter, but not Desulfotomaculum, indicating that Geobacter acquired energy via syntrophic interaction with methanogenic archaea. Although electron acceptor compounds such as sulfate and iron oxides have been thought to suppress methanogenesis, this study revealed that coexistence of sulfate and iron oxide can promote methanogenesis by biomineralization of (semi)conductive iron sulfides that enable methanogenesis via electric syntrophy.
Topics: Desulfotomaculum; Ferrous Compounds; Geobacter; Methane; Methanosarcina; Microbial Consortia; Microbial Interactions; Minerals; Oryza; Water Microbiology
PubMed: 29877051
DOI: 10.1002/mbo3.647 -
PLoS Computational Biology Nov 2021The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in...
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
Topics: Algorithms; Bacteroidetes; Bifidobacterium adolescentis; Computational Biology; Computer Simulation; Databases, Factual; Escherichia coli; Faecalibacterium prausnitzii; Gastrointestinal Microbiome; Humans; Metabolic Networks and Pathways; Microbiota; Models, Biological; Peptococcaceae; Synthetic Biology
PubMed: 34723959
DOI: 10.1371/journal.pcbi.1009060 -
GeroScience Apr 2022Recently, aging is considered a risk factor for various diseases. Although changes in the intestinal microbiota along with aging are thought to associate with the...
Recently, aging is considered a risk factor for various diseases. Although changes in the intestinal microbiota along with aging are thought to associate with the increased disease risk, mechanisms that cause age-related transition of the intestinal microbiota remain unknown. This study aims to clarify relationships between the amount of human defensin 5 (HD5), a Paneth cell α-defensin, which is known to regulate the intestinal microbiota, and age-related differences of the intestinal microbiota composition. Fecal samples from 196 healthy Japanese (35 to 81 years old) were collected and measured HD5 concentration. HD5 concentration in the elderly group (age > 70 years old) was significantly lower than the middle-aged group (age ≤ 70 years old). Furthermore, individual age was negatively correlated with HD5 concentration (r = - 0.307, p < 0.001). In β-diversity, the intestinal microbiota of the elderly showed a significantly different composition compared to the middle-aged. At the genus level, relative abundance of Collinsella, Alistipes, Peptococcaceae; unassigned, Lactobacillus, Lactococcus, Weissella, Christensenellaceae R-7 group, Megasphaera, and [Eubacterium] eligens group was significantly higher, and Lachnospiraceae; unassigned, Blautia, Anaerostipes, Fusicatenibacter, Dorea, and Faecalibacterium was significantly lower in the elderly compared to the middle-aged. In addition, HD5 concentration was negatively correlated with Alistipes, Peptococcaceae; unassigned, and Christensenellaceae R-7 group and positively correlated with Lachnospiraceae; unassigned and Dorea. These results provide novel insights into the immunosenescence of enteric innate immunity, indicating low HD5 is suggested to contribute to the age-related differences in the intestinal microbiota and may relate to increased risk of diseases in elderly people.
Topics: Adult; Aged; Aged, 80 and over; Defensins; Feces; Gastrointestinal Microbiome; Humans; Japan; Middle Aged; alpha-Defensins
PubMed: 34105106
DOI: 10.1007/s11357-021-00398-y -
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 -
BioMed Research International 2021The incidence of small intestinal injury caused by low-dose aspirin (LDA) is high, but the pathogenesis and intervention measures of it have not been elucidated. Recent...
BACKGROUND
The incidence of small intestinal injury caused by low-dose aspirin (LDA) is high, but the pathogenesis and intervention measures of it have not been elucidated. Recent studies have found gut microbiota to be closely associated with onset and development of NSAID-induced intestinal injury. However, studies of the changes in the gut microbiota of rats with LDA-related intestinal injury have been lacking recently. In this study, we investigated fecal 16S rRNA gene sequencing analysis of changes in the gut microbiota of rats with LDA-related intestinal injury.
METHODS
Sprague-Dawley (SD) rat models of small intestinal injury were established by intragastric administration of LDA. The small intestinal tissues and the fecal samples were harvested. The fecal samples were then analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. The gut microbiota composition and diversity were analyzed and compared using principal coordinate analysis (PCoA), nonmetric multidimensional scaling (NMDS) analysis, the unweighted pair-group method with arithmetic mean (UPGMA) clustering analysis, multivariate statistical analysis (ANOSIM, MetaStats, and LEfSe), and spatial statistics.
RESULTS
The LDA rat model was successfully established. Decreased Firmicutes and increased Bacteroidetes abundances in rats with LDA-induced small intestinal injury were revealed. MetaStats analysis between the before administration of LDA (CG) and after administration of LDA (APC) groups showed that the intestinal floras exhibiting significant differences ( < 0.05, < 0.1) were Firmicutes, Bacteroides, Cyanobacteria, Melainabacteria, Coriobacteriia, Bacteroidia, Bacteroidales, Eubacteriaceae, and Streptococcaceae. In addition, the bacterial taxa showing significant differences between the control (NS) and APC groups were Firmicutes, Bacteroides, Verrucomicrobiaceae and Peptococcaceae.
CONCLUSIONS
The alterations in the gut microbiota composition and diversity of rats with LDA-related intestinal injury were found in the present study. The change of gut microbiota in LDA-related intestinal injury will lay the foundation for further research on the function and signaling pathways of the intestinal flora and promote the use of intestinal flora as drug targets to treat LDA-induced small intestinal injury.
Topics: Animals; Aspirin; Biodiversity; Cluster Analysis; Dose-Response Relationship, Drug; Feces; Gastrointestinal Microbiome; Intestinal Mucosa; Intestines; Male; Phylogeny; Principal Component Analysis; RNA, Ribosomal, 16S; Rats, Sprague-Dawley; Sequence Analysis, RNA; Staining and Labeling; Tissue Adhesions; Ulcer; Rats
PubMed: 33954200
DOI: 10.1155/2021/8848686 -
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 -
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 -
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