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Anaerobe Dec 2021The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools,...
The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.
Topics: Abscess; Adolescent; Adult; Anti-Bacterial Agents; Appendicitis; Blood Culture; Disease Management; Disease Susceptibility; Female; Humans; Male; Methanobrevibacter; Middle Aged; Molecular Typing; RNA, Ribosomal, 16S; Tomography, X-Ray Computed; Young Adult
PubMed: 34743984
DOI: 10.1016/j.anaerobe.2021.102470 -
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 -
Waste Management (New York, N.Y.) Nov 2021Transitions in microbial community structure in response to increasing ammonia concentrations were determined by monitoring mesophilic anaerobic digesters seeded with a...
Transitions in microbial community structure in response to increasing ammonia concentrations were determined by monitoring mesophilic anaerobic digesters seeded with a predominantly acetoclastic methanogenic community from a sewage sludge digester. Ammonia concentration was raised by switching the feed to source segregated domestic food waste and applying two organic loading rates (OLR) and hydraulic retention times (HRT) in paired digesters. One of each pair was dosed with trace elements (TE) known to be essential to the transition, with the other unsupplemented digester acting as a control. Samples taken during the trial were used to determine the metabolic pathway to methanogenesis using C labelled acetate. Partitioning of C between the product gases was interpreted via an equation to indicate the proportion produced by acetoclastic and hydrogenotrophic routes. Archaeal and selected bacterial groups were identified by 16S rRNA sequencing, to determine relative abundance and diversity. Acclimatisation for digesters with TE was relatively smooth, but OLR and HRT influenced both metabolic route and community structure. The C ratio could be used quantitatively and, when interpreted alongside archaeal community structure, showed that at longer HRT and lower loading Methanobacteriaceae were dominant and hydrogenotrophic activity accounted for 77% of methane production. At the higher OLR and shorter HRT, Methanosarcinaceae were dominant with the C ratio indicating simultaneous production of methane by acetoclastic and hydrogenotrophic pathways: the first reported observation of this in digestion under mesophilic conditions. Digesters without TE supplementation showed similar initial changes but, as expected failed to complete the transition to stable operation.
Topics: Ammonium Compounds; Anaerobiosis; Bioreactors; Food; Metabolic Networks and Pathways; Methane; RNA, Ribosomal, 16S; Refuse Disposal; Sewage
PubMed: 34619622
DOI: 10.1016/j.wasman.2021.09.017 -
Microbiome Sep 2021Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an...
BACKGROUND
Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE).
RESULTS
We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods.
CONCLUSIONS
We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
Topics: Archaea; Dental Calculus; Humans; Metagenome; Methanobrevibacter; Middle Aged; Phylogeny
PubMed: 34593021
DOI: 10.1186/s40168-021-01132-8 -
Microbiome Sep 2021Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human...
BACKGROUND
Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood.
RESULTS
We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH breath content 5-75 ppm) and low emitters (CH < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis.
CONCLUSIONS
This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.
Topics: Adult; Animals; Female; Formates; Gastrointestinal Tract; Humans; Male; Metagenomics; Methane; Methanobrevibacter; Rumen; Young Adult
PubMed: 34560884
DOI: 10.1186/s40168-021-01130-w -
Applied and Environmental Microbiology Oct 2021Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO to CH. Setting low cathode potentials is essential for this...
Electromethanogenesis refers to the process whereby methanogens utilize current for the reduction of CO to CH. Setting low cathode potentials is essential for this process. In this study, we tested if magnetite, an iron oxide mineral widespread in the environment, can facilitate the adaptation of methanogen communities to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from paddy field soil. We elevated cathode potentials stepwise from the initial -0.6 V versus the standard hydrogen electrode (SHE) to -0.5 V and then to -0.4 V over the 130 days of acclimation. Only weak current consumption and CH production were observed in the bioreactors without magnetite. However, significant current consumption and CH production were recorded in the magnetite bioreactors. The robustness of electroactivity of the magnetite bioreactors was not affected by the elevation of cathode potentials from -0.6 V to -0.4 V. However, the current consumption and CH production were halted in the bioreactors without magnetite when the cathode potentials were elevated to -0.4 V. Methanogens related to were enriched on the cathode surfaces of magnetite bioreactors at -0.4 V, while relatively dominated in the bioreactors without magnetite. also increased in the magnetite bioreactors but stayed off electrodes at -0.4 V. Apparently, the magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite, spp. can adapt to the high cathode potentials, performing efficient electromethanogenesis. Converting CO to CH through bioelectrochemistry is a promising approach to the development of green energy biotechnology. This process, however, requires low cathode potentials, which entails a cost. In this study, we tested if magnetite, a conductive iron mineral, can facilitate the adaptation of methanogens to the elevation of cathode potentials. In two-chamber reactors constructed by using inoculants obtained from paddy field soil, biocathodes developed robustly in the presence of magnetite, whereas only weak activities in CH production and current consumption were observed in the bioreactors without magnetite. The elevation of cathode potentials did not affect the robustness of electroactivity of the magnetite bioreactors over the 130 days of acclimation. strains were identified as the key methanogens associated with the cathode surfaces during the operation at high potentials. The findings reported in this study shed new light on the adaptation of methanogen communities to the elevated cathode potentials in the presence of magnetite.
Topics: Bioreactors; Biotechnology; Carbon Dioxide; Electrodes; Ferrosoferric Oxide; Methane; Methanobacterium; Methanosarcina; Methanospirillum
PubMed: 34432490
DOI: 10.1128/AEM.01488-21 -
Osteoarthritis and Cartilage Dec 2021There is considerable evidence for relationship between gut microbiota and osteoarthritis (OA), but no studies have investigated their causal relationship.
OBJECTIVE
There is considerable evidence for relationship between gut microbiota and osteoarthritis (OA), but no studies have investigated their causal relationship.
METHOD
This study utilized large-scale genome-wide association studies (GWAS) summary statistics to evaluate the causal association between gut microbiota and OA risk. Specifically, two-sample Mendelian randomization (MR) approach was used to identify the causal microbial taxa for OA. Comprehensively sensitive analyses were performed to validate the robustness of results and novel multivariable MR analyses were further conducted to ensure the independence of causal association. Reverse-direction MR analyses were performed to rule out the possibility of reverse associations. Finally, enrichment analyses were used to investigate the biofunction.
RESULTS
After correction, three microbial taxa were identified to be causally associated with diverse joint OA (P < 0.100), namely Methanobacteriaceae family for knee OA (P = 0.043) and any OA (P = 0.028), Desulfovibrionales order for knee OA (P = 0.045) and Ruminiclostridium5 genus for knee OA (P = 0.063). In addition, we also identified five suggestive microbial taxa that were significant with three different methods under the nominal significance (P < 0.05). Sensitive analysis excluded the influence of heterogeneity and horizontal pleiotropy and multivariable MR analysis ruled out the possibility of horizontal pleiotropy of BMI. GO enrichment analysis illustrates the protective mechanism of the identified taxa against OA.
CONCLUSIONS
This study found that several microbial taxa were causally associated with diverse joint OA. The results enhanced our understanding of gut microbiota in the pathology of OA.
Topics: Causality; Gastrointestinal Microbiome; Genome-Wide Association Study; Humans; Mendelian Randomization Analysis; Osteoarthritis
PubMed: 34425228
DOI: 10.1016/j.joca.2021.08.003 -
Ecology and Evolution Aug 2021Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and...
Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic A gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the - wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the wetland and the wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.
PubMed: 34367583
DOI: 10.1002/ece3.7842 -
Scientific Reports Jul 2021Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in...
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.
Topics: Bayes Theorem; Cytochromes; Electron Transport; Electrons; Geobacter; Hydrogen; Machine Learning; Metabolic Networks and Pathways; Methane; Methanobacterium
PubMed: 34302023
DOI: 10.1038/s41598-021-94628-0 -
Microorganisms Jun 2021A sufficient supply of phosphorus (P) to pigs in livestock farming is based on the optimal use of plant-based phytate and mineral P supplements to ensure proper growth...
A sufficient supply of phosphorus (P) to pigs in livestock farming is based on the optimal use of plant-based phytate and mineral P supplements to ensure proper growth processes and bone stability. However, a high P supplementation might bear the risk of higher environmental burden due to the occurrence of excess P and phytate degradation products in manure. In this context, the intestinal microbiota is of central importance to increase P solubility, to employ non-mineral P by the enzymatic degradation of phytate, and to metabolize residual P. A feeding experiment was conducted in which piglets were fed diets with different P levels, resulting in three groups with low, medium (covering requirements), and high concentrations of available P. Samples from caecum and colon digesta were analysed for microbial composition and phytate breakdown to estimate the microbial contribution to metabolize P sources. In terms of identified operational taxonomic units (OTU), caecum and colon digesta under the three feeding schemes mainly overlap in their core microbiome. Nevertheless, different microbial families correlate with increased dietary P supply. Specifically, microbes of , , and were found significantly differentially abundant in the large intestine across the dietary treatments. Moreover, members of the families , and might contribute to the observed phytate degradation in animals fed a low P diet. In this sense, the targeted manipulation of the intestinal microbiota by feeding measures offers possibilities for the optimization of intestinal phytate and P utilization.
PubMed: 34205896
DOI: 10.3390/microorganisms9061197