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The ISME Journal Apr 2020Dichloromethane (DCM) is an anthropogenic pollutant with ozone destruction potential that is also formed naturally. Under anoxic conditions, fermentation of DCM to...
Dichloromethane (DCM) is an anthropogenic pollutant with ozone destruction potential that is also formed naturally. Under anoxic conditions, fermentation of DCM to acetate and formate has been reported in axenic culture Dehalobacterium formicoaceticum, and to acetate, H and CO in mixed culture RM, which harbors the DCM degrader 'Candidatus Dichloromethanomonas elyunquensis'. RM cultures produced 28.1 ± 2.3 μmol of acetate from 155.6 ± 9.3 μmol DCM, far less than the one third (i.e., about 51.9 µmol) predicted based on the assumed fermentation model, and observed in cultures of Dehalobacterium formicoaceticum. Temporal metabolite analyses using gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy revealed that no C-labeled acetate was formed in C-DCM-grown RM cultures, indicating acetate was not a direct product of DCM metabolism. The data were reconciled with DCM mineralization and H consumption via CO reduction to acetate and methane by homoacetogenic and methanogenic partner populations, respectively. In contrast, Dehalobacterium formicoaceticum produced C-labeled acetate and formate from C-DCM, consistent with a fermentation pathway. Free energy change calculations predicted that organisms with the mineralization pathway are the dominant DCM consumers in environments with H <100 ppmv. These findings have implications for carbon and electron flow in environments where DCM is introduced through natural production processes or anthropogenic activities.
Topics: Acetates; Anaerobiosis; Bacteria, Anaerobic; Biodegradation, Environmental; Carbon; Carbon Dioxide; Euryarchaeota; Fermentation; Hydrogen; Methane; Methylene Chloride; Peptococcaceae
PubMed: 31907367
DOI: 10.1038/s41396-019-0579-5 -
Microbial Genomics Oct 2022Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for...
Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between (.) and the intestinal microbiota might influence colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with in -specific phage-free chickens under standardized conditions and special biosafety precautions.Therefore, 12 artificially infected ( inoculum with a challenge dose of 7.64 log c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No -specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between -negative and -positive chickens. The factor chickens' infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (=0.015). The strongest difference between -non-infected and -infected birds was observed for the family whose presence in -infected birds could not be demonstrated. Further, several genera of the family appeared to be depressed in its abundance due to infection. A negative correlation was found between R-7 group and in -colonised chickens, both genera potentially competing for substrate. This makes R-7 group highly interesting for further studies that aim to find control options for infections and assess the relevance of this finding for chicken health and colonization.
Topics: Animals; Bacteriophages; Campylobacter; Campylobacter Infections; Campylobacter jejuni; Chickens; Humans; Microbiota; Mucous Membrane; Poultry Diseases; RNA, Ribosomal, 16S
PubMed: 36190827
DOI: 10.1099/mgen.0.000874 -
Applied Microbiology and Biotechnology Jun 2019Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide...
Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.
Topics: Clostridium; Culture Media; Desulfotomaculum; Gene Expression; Genes, Bacterial; Metabolic Engineering; Metabolic Networks and Pathways; Recombinant Proteins; Vitamins
PubMed: 30972463
DOI: 10.1007/s00253-019-09763-6 -
PeerJ 2019Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CHCl) are of great interest for potential bioremediation applications. A...
Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CHCl) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRT sequencing of DCMF allowed , gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
PubMed: 31592187
DOI: 10.7717/peerj.7775 -
Frontiers in Microbiology 2017Soil salinization due to seawater intrusion along coastal areas is an increasing threat to rice cultivation worldwide. While the detrimental impact on rice growth and...
Soil salinization due to seawater intrusion along coastal areas is an increasing threat to rice cultivation worldwide. While the detrimental impact on rice growth and yield has been thoroughly studied, little is known about how severe salinity affects structure and function of paddy soil microbial communities. Here, we examined their short-term responses to half- and full-strength seawater salinity in controlled laboratory experiments. Slurry microcosms were incubated under anoxic conditions, with rice straw added as carbon source. Stress exposure time was for 2 days after a pre-incubation period of 7 days. Relative to the control, moderate (300 mM NaCl) and high (600 mM NaCl) salt stress suppressed both net consumption of acetate and methane production by 50% and 70%, respectively. Correspondingly, community-wide mRNA expression decreased by 50-65%, with significant changes in relative transcript abundance of family-level groups. mRNA turnover was clearly more responsive to salt stress than rRNA dynamics. Among bacteria, Clostridiaceae were most abundant and the only group whose transcriptional activity was strongly stimulated at 600 mM NaCl. In particular, clostridial mRNA involved in transcription/translation, fermentation, uptake and biosynthesis of compatible solutes, and flagellar motility was significantly enriched in response salt stress. None of the other bacterial groups were able to compete at 600 mM NaCl. Their responses to 300 mM NaCl were more diverse. Lachnospiraceae increased, Ruminococcaceae maintained, and Peptococcaceae, Veillonellaceae, and Syntrophomonadaceae decreased in relative mRNA abundance. Among methanogens, Methanosarcinaceae were most dominant. Relative to other family-level groups, salt stress induced a significant enrichment of transcripts related to the CO dehydrogenase/acetyl-coenzyme A synthase complex, methanogenesis, heat shock, ammonium uptake, and thermosomes, but the absolute abundance of methanosarcinal mRNA decreased. Most strikingly, the transcriptional activity of the Methanocellaceae was completely suppressed already at 300 mM NaCl. Apparently, the key taxonomic groups involved in the methanogenic breakdown of plant polymers significantly differ in their ability to cope with severe salt stress. Presumably, this different ability is directly linked to differences in their genetic potential and metabolic flexibility to reassign available energy resources for cellular adaptation to salt stress.
PubMed: 28400748
DOI: 10.3389/fmicb.2017.00400 -
Applied and Environmental Microbiology May 2017Iron artifacts are common among the findings of archaeological excavations. The corrosion layer formed on these objects requires stabilization after their recovery,...
Iron artifacts are common among the findings of archaeological excavations. The corrosion layer formed on these objects requires stabilization after their recovery, without which the destruction of the item due to physicochemical damage is likely. Current technologies for stabilizing the corrosion layer are lengthy and generate hazardous waste products. Therefore, there is a pressing need for an alternative method for stabilizing the corrosion layer on iron objects. The aim of this study was to evaluate an alternative conservation-restoration method using bacteria. For this, anaerobic iron reduction leading to the formation of stable iron minerals in the presence of chlorine was investigated for two strains of (strains TCE1 and LBE). Iron reduction was observed for soluble Fe(III) phases as well as for akaganeite, the most troublesome iron compound in the corrosion layer of archaeological iron objects. In terms of biogenic mineral production, differential efficiencies were observed in assays performed on corroded iron coupons. Strain TCE1 produced a homogeneous layer of vivianite covering 80% of the corroded surface, while on the coupons treated with strain LBE, only 10% of the surface was covered by the same mineral. Finally, an attempt to reduce iron on archaeological objects was performed with strain TCE1, which led to the formation of both biogenic vivianite and magnetite on the surface of the artifacts. These results demonstrate the potential of this biological treatment for stabilizing archaeological iron as a promising alternative to traditional conservation-restoration methods. Since the Iron Age, iron has been a fundamental material for the building of objects used in everyday life. However, due to its reactivity, iron can be easily corroded, and the physical stability of the object built is at risk. This is particularly true for archaeological objects on which a potentially unstable corrosion layer is formed during the time the object is buried. After excavation, changes in environmental conditions (e.g., higher oxygen concentration or lower humidity) alter the stability of the corrosion layer and can lead to the total destruction of the object. In this study, we demonstrate the feasibility of an innovative treatment based on bacterial iron reduction and biogenic mineral formation to stabilize the corrosion layer and protect these objects.
Topics: Archaeology; Corrosion; Desulfitobacterium; Ferric Compounds; Iron; Oxidation-Reduction
PubMed: 28283522
DOI: 10.1128/AEM.03478-16 -
Nutrients Nov 2022This study aims to analyze the relationship between gut microbiota composition and health parameters through specific biochemical markers and food consumption patterns...
This study aims to analyze the relationship between gut microbiota composition and health parameters through specific biochemical markers and food consumption patterns in the Spanish population. This research includes 60 Spanish adults aged 47.3 ± 11.2 years old. Biochemical and anthropometric measurements, and a self-referred dietary survey (food frequency questionnaire), were analyzed and compared with the participant´s gut microbiota composition analyzed by 16s rDNA sequencing. Several bacterial strains differed significantly with the biochemical markers analyzed, suggesting an involvement in the participant´s metabolic health. Lower levels of Lactobacillaceae and Oscillospiraceae and an increase in Pasteurellaceae, , and were observed in individuals with higher AST levels. Higher levels of the Christensenellaceae and a decrease in Peptococcaceae were associated with higher levels of HDL-c. High levels of and and low levels of were found in individuals with higher insulin levels. This study also identified associations between bacteria and specific food groups, such as an increase in lactic acid bacteria with the consumption of fermented dairy products or an increase in Verrucomicrobiaceae with the consumption of olive oil. In conclusion, this study reinforces the idea that specific food groups can favorably modulate gut microbiota composition and have an impact on host´s health.
Topics: Adult; Humans; Middle Aged; Gastrointestinal Microbiome; Diet; Verrucomicrobia; Cultured Milk Products; Lactobacillaceae
PubMed: 36500996
DOI: 10.3390/nu14234966 -
The ISME Journal Jan 2011Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through...
Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium inside a hyper-mesophilic (that is, between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified β-oxidation to H(2)/CO(2) and acetate. These intermediates are converted to CH(4)/CO(2) by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to CO(2)/H(2) and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H(2)-producing syntroph-methanogen partnership that may serve to improve community stability.
Topics: Biodegradation, Environmental; Bioreactors; Ecosystem; Euryarchaeota; Metagenome; Methane; Peptococcaceae; Phthalic Acids; RNA, Ribosomal, 16S
PubMed: 20686509
DOI: 10.1038/ismej.2010.125 -
Frontiers in Cellular and Infection... 2017The oral microbiota plays a critical role in both local and systemic inflammation. Metabolic syndrome (MetS) is characterized by low-grade inflammation, and many studies...
The oral microbiota plays a critical role in both local and systemic inflammation. Metabolic syndrome (MetS) is characterized by low-grade inflammation, and many studies have been conducted on the gut microbiota from stool specimens. However, the etiological role of the oral microbiota in the development of MetS is unclear. In this study, we analyzed the oral and gut microbiome from 228 subgingival plaque and fecal samples from a Korean twin-family cohort with and without MetS. Significant differences in microbial diversity and composition were observed in both anatomical niches. However, a host genetic effect on the oral microbiota was not observed. A co-occurrence network analysis showed distinct microbiota clusters that were dependent on the MetS status. A comprehensive analysis of the oral microbiome identified and as bacteria enriched in subjects with MetS and as bacteria abundant in healthy controls. Validation of the identified oral bacteria by quantitative PCR (qPCR) showed that healthy controls possessed significantly lower levels of . ( = 0.023) and a higher ratio of to ( < 0.05) than MetS subjects. Our results support that local oral microbiota can be associated with systemic disorders. The microbial biomarkers identified in this study would aid in determination of which individuals develop chronic diseases from their MetS and contribute to strategic disease management.
Topics: Adult; Aged; Biomarkers; Carnobacteriaceae; Dental Plaque; Feces; Female; Humans; Male; Metabolic Syndrome; Microbiota; Middle Aged; Mouth; Neisseria; Peptococcus; Real-Time Polymerase Chain Reaction
PubMed: 29326886
DOI: 10.3389/fcimb.2017.00516 -
PloS One 2013Links between the gut microbiota and host metabolism have provided new perspectives on obesity. We previously showed that the link between the microbiota and fat...
Links between the gut microbiota and host metabolism have provided new perspectives on obesity. We previously showed that the link between the microbiota and fat deposition is age- and time-dependent subject to microbial adaptation to diet over time. We also demonstrated reduced weight gain in diet-induced obese (DIO) mice through manipulation of the gut microbiota with vancomycin or with the bacteriocin-producing probiotic Lactobacillus salivarius UCC118 (Bac(+)), with metabolic improvement achieved in DIO mice in receipt of vancomycin. However, two phases of weight gain were observed with effects most marked early in the intervention phase. Here, we compare the gut microbial populations at the early relative to the late stages of intervention using a high throughput sequencing-based analysis to understand the temporal relationship between the gut microbiota and obesity. This reveals several differences in microbiota composition over the intervening period. Vancomycin dramatically altered the gut microbiota composition, relative to controls, at the early stages of intervention after which time some recovery was evident. It was also revealed that Bac(+) treatment initially resulted in the presence of significantly higher proportions of Peptococcaceae and significantly lower proportions of Rikenellaceae and Porphyromonadaceae relative to the gut microbiota of L. salivarius UCC118 bacteriocin negative (Bac(-)) administered controls. These differences were no longer evident at the later time. The results highlight the resilience of the gut microbiota and suggest that interventions may need to be monitored and continually adjusted to ensure sustained modification of the gut microbiota.
Topics: Animals; Biodiversity; Colony Count, Microbial; Diet; Gastrointestinal Tract; Male; Mice; Mice, Inbred C57BL; Microbiota; Obesity; Phylogeny; Principal Component Analysis; Time Factors; Vancomycin; Weight Gain
PubMed: 23762426
DOI: 10.1371/journal.pone.0065790