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PloS One 2024The economic impact of gastrointestinal (GI) nematode infections on livestock production is well documented worldwide. Increasing evidence supports the hypothesis that...
The economic impact of gastrointestinal (GI) nematode infections on livestock production is well documented worldwide. Increasing evidence supports the hypothesis that parasite colonization induces significant changes in the GI tract environment and, therefore, in the landscape where the microbiota and parasites occur. Understanding the interactions between bacterial and parasite populations in the digestive tract of livestock may be useful to design parasite control strategies based on microbiota modification. The aims of this work were to investigate the impact of the oxytetracycline-mediated manipulation of the gut microbial community on the composition of GI nematode populations in naturally infected sheep and to explore changes in the GI microbial communities after nematode population treatment with the anthelmintic compound monepantel. Extensive manipulation of the GI microbiota with a therapeutic dose of the long-acting oxytetracycline formulation did not induce significant changes in the GI nematode burden. The gut microbiota of treated animals returned to control levels 17 days after treatment, suggesting strong resilience of the sheep microbial community to antibiotic-mediated microbiota perturbation. A significant decrease of the bacterial Mycoplasmataceae family (Log2FC = -4, Padj = 0.001) and a marked increase of the Methanobacteriaceae family (Log2FC = 2.9, Padj = 0.018) were observed in the abomasum of sheep receiving the monepantel treatment. While a comprehensive evaluation of the interactions among GI mycoplasma, methanobacteria and nematode populations deserves further assessment, the bacteria-nematode population interactions should be included in future control programs in livestock production. Understanding how bacteria and parasites may influence each other in the GI tract environment may substantially contribute to the knowledge of the role of microbiota composition in nematode parasite establishment and the role of the parasites in the microbiota composition.
Topics: Animals; Sheep; Gastrointestinal Microbiome; Sheep Diseases; Nematode Infections; Nematoda; Oxytetracycline; Gastrointestinal Tract; Aminoacetonitrile; Bacteria
PubMed: 38935803
DOI: 10.1371/journal.pone.0306390 -
Gut Microbes 2024The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms,...
The gut microbiota has been implicated as a driver of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Recently we described, mucosal biofilms, signifying alterations in microbiota composition and bile acid (BA) metabolism in IBS and ulcerative colitis (UC). Luminal oxygen concentration is a key factor in the gastrointestinal (GI) ecosystem and might be increased in IBS and UC. Here we analyzed the role of archaea as a marker for hypoxia in mucosal biofilms and GI homeostasis. The effects of archaea on microbiome composition and metabolites were analyzed via amplicon sequencing and untargeted metabolomics in 154 stool samples of IBS-, UC-patients and controls. Mucosal biofilms were collected in a subset of patients and examined for their bacterial, fungal and archaeal composition. Absence of archaea, specifically , correlated with disrupted GI homeostasis including decreased microbial diversity, overgrowth of facultative anaerobes and conjugated secondary BA. IBS-D/-M was associated with absence of archaea. Presence of correlated with and epithelial short chain fatty acid metabolism and decreased levels of . Absence of fecal may indicate a less hypoxic GI environment, reduced fatty acid oxidation, overgrowth of facultative anaerobes and disrupted BA deconjugation. Archaea and could distinguish distinct subtypes of mucosal biofilms. Further research on the connection between archaea, mucosal biofilms and small intestinal bacterial overgrowth should be performed.
Topics: Humans; Biofilms; Gastrointestinal Microbiome; Archaea; Adult; Middle Aged; Female; Male; Bacteria; Feces; Colon; Methanobrevibacter; Colitis, Ulcerative; Irritable Bowel Syndrome; Aged; Intestinal Mucosa; Ileum; Fatty Acids, Volatile; Young Adult; Bile Acids and Salts
PubMed: 38825783
DOI: 10.1080/19490976.2024.2359500 -
Food Research International (Ottawa,... Jul 2024The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and...
The microorganisms of the pit mud (PM) of Nongxiangxing baijiu (NXXB) have an important role in the synthesis of flavor substances, and they determine attributes and quality of baijiu. Herein, we utilize metagenomics and genome-scale metabolic models (GSMMs) to investigate the microbial composition, metabolic functions in PM microbiota, as well as to identify microorganisms and communities linked to flavor compounds. Metagenomic data revealed that the most prevalent assembly of bacteria and archaea was Proteiniphilum, Caproicibacterium, Petrimonas, Lactobacillus, Clostridium, Aminobacterium, Syntrophomonas, Methanobacterium, Methanoculleus, and Methanosarcina. The important enzymes ofPMwere in bothGH and GT familymetabolism. A total of 38 high-quality metagenome-assembled genomes (MAGs) were obtained, including those at the family level (n = 13), genus level (n = 17), and species level (n = 8). GSMMs of the 38 MAGs were then constructed. From the GSMMs, individual and community capabilities respectively were predicted to be able to produce 111 metabolites and 598 metabolites. Twenty-three predicted metabolites were consistent with the metabonomics detected flavors and served as targets. Twelve sub-community of were screened by cross-feeding of 38 GSMMs. Of them, Methanobacterium, Sphaerochaeta, Muricomes intestini, Methanobacteriaceae, Synergistaceae, and Caloramator were core microorganisms for targets in each sub-community. Overall, this study of metagenomic and target-community screening could help our understanding of the metabolite-microbiome association and further bioregulation of baijiu.
Topics: Metagenomics; Microbiota; Bacteria; Archaea; Flavoring Agents; Metagenome
PubMed: 38823882
DOI: 10.1016/j.foodres.2024.114507 -
Frontiers in Microbiology 2024The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers.
INTRODUCTION
The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers.
METHODS
Metagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers ( = 20) with similar body weights and ages from grass-fed and grain-fed systems.
RESULTS
The grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system.
CONCLUSION
These results could help manipulate and regulate feed efficiency in Sanhe cattle.
PubMed: 38803375
DOI: 10.3389/fmicb.2024.1336278 -
Chemosphere Jun 2024The CO bioelectromethanosynthesis via two-chamber microbial electrolysis cell (MEC) holds tremendous potential to solve the energy crisis and mitigate the greenhouse gas...
The CO bioelectromethanosynthesis via two-chamber microbial electrolysis cell (MEC) holds tremendous potential to solve the energy crisis and mitigate the greenhouse gas emissions. However, the membrane fouling is still a big challenge for CO bioelectromethanosynthesis owing to the poor proton diffusion across membrane and high inter-resistance. In this study, a new MEC bioreactor with biogas recirculation unit was designed in the cathode chamber to enhance secondary-dissolution of CO2 while mitigating the contaminant adhesion on membrane surface. Biogas recirculation improved CO re-dissolution, reduced concentration polarization, and facilitated the proton transmembrane diffusion. This resulted in a remarkable increase in the cathodic methane production rate from 0.4 mL/L·d to 8.5 mL/L·d. A robust syntrophic relationship between anodic organic-degrading bacteria (Firmicutes 5.29%, Bacteroidetes 25.90%, and Proteobacteria 6.08%) and cathodic methane-producing archaea (Methanobacterium 65.58%) enabled simultaneous organic degradation, high CO bioelectromethanosynthesis, and renewable energy storage.
Topics: Carbon Dioxide; Bioreactors; Methane; Biofuels; Electrolysis; Electrodes; Bioelectric Energy Sources; Methanobacterium; Membranes, Artificial; Proteobacteria
PubMed: 38697567
DOI: 10.1016/j.chemosphere.2024.142119 -
FEMS Microbiology Ecology May 2024The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage...
The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.
Topics: Methane; Groundwater; Natural Gas; Hydrogen; Sulfates; Methanobacteriaceae; Carbon Dioxide; Bacteria; Hydrogen-Ion Concentration; Water Microbiology
PubMed: 38658197
DOI: 10.1093/femsec/fiae066 -
Applied and Environmental Microbiology May 2024A new variant of was isolated from an anaerobic digester using enrichment cultivation in anaerobic conditions. The new isolate was taxonomically identified via 16S rRNA...
A new variant of was isolated from an anaerobic digester using enrichment cultivation in anaerobic conditions. The new isolate was taxonomically identified via 16S rRNA gene sequencing and tagged as BSEL. The whole genome of the new variant was sequenced and assembled. Genomic variations between the BSEL strain and the type strain were discovered, suggesting evolutionary adaptations of the BSEL strain that conferred advantages while growing under a low concentration of nutrients. BSEL displayed the highest specific growth rate ever reported for the species (0.27 ± 0.03 h) using carbon dioxide (CO) as unique carbon source and hydrogen (H) as electron donor. BSEL grew at this rate in an environment with ammonium (NH) as sole nitrogen source. The minerals content required to cultivate the BSEL strain was relatively low and resembled the ionic background of tap water without mineral supplements. Optimum growth rate for the new isolate was observed at 64°C and pH 8.3. In this work, it was shown that wastewater from a wastewater treatment facility can be used as a low-cost alternative medium to cultivate BSEL. Continuous gas fermentation fed with a synthetic biogas mimic along with H in a bubble column bioreactor using BSEL as biocatalyst resulted in a CO conversion efficiency of 97% and a final methane (CH) titer of 98.5%, demonstrating the ability of the new strain for upgrading biogas to renewable natural gas.IMPORTANCEAs a methanogenic archaeon, uses CO as electron acceptor, producing CH as final product. The metabolism of can be harnessed to capture CO from industrial emissions, besides producing a drop-in renewable biofuel to substitute fossil natural gas. If used as biocatalyst in new-generation CO sequestration processes, has the potential to accelerate the decarbonization of the energy generation sector, which is the biggest contributor of CO emissions worldwide. Nonetheless, the development of CO sequestration archaeal-based biotechnology is still limited by an uncertainty in the requirements to cultivate methanogenic archaea and the unknown longevity of archaeal cultures. In this study, we report the adaptation, isolation, and phenotypic characterization of a novel variant of , which is capable of maximum growth with minimal nutrients input. Our findings demonstrate the potential of this variant for the production of renewable natural gas, paving the way for the development of more efficient and sustainable CO sequestration processes.
Topics: Methanobacteriaceae; Carbon Dioxide; RNA, Ribosomal, 16S; Genome, Archaeal; Phylogeny; Phenotype; Wastewater; Methane; Nutrients
PubMed: 38619268
DOI: 10.1128/aem.00268-24 -
International Urology and Nephrology Apr 2024Recent studies demonstrated that chronic prostatitis (CP) is closely related to the gut microbiota (GM). Nevertheless, the causal relationship between GM and CP has not...
BACKGROUND
Recent studies demonstrated that chronic prostatitis (CP) is closely related to the gut microbiota (GM). Nevertheless, the causal relationship between GM and CP has not been fully elucidated. Therefore, the two-sample Mendelian randomization (MR) analysis was employed to investigate this association.
METHODS
The summary data of gut microbiota derived from a genome-wide association study (GWAS) involving 18,340 individuals in the MiBioGen study served as the exposure, and the corresponding summary statistics for CP risk, representing the outcome, were obtained from the FinnGen databases (R9). The causal effects between GM and CP were estimated using the inverse-variance weighted (IVW) method supplemented with MR-Egger, weighted median, weighted mode, and simple mode methods. Additionally, the false discovery rate (FDR) correction was performed to adjust results. The detection and quantification of heterogeneity and pleiotropy were accomplished through the MR pleiotropy residual sum and outlier method, Cochran's Q statistics, and MR-Egger regression.
RESULTS
The IVW estimates indicated that a total of 11 GM taxa were related to the risk of CP. Seven of them was correlated with an increased risk of CP, while the remained linked with a decreased risk of CP. However, only Methanobacteria (OR 0.86; 95% CI 0.74-0.99), Methanobacteriales (OR 0.86; 95% CI 0.74-0.99), NB1n (OR 1.16; 95% CI 1.16-1.34), Methanobacteriaceae (OR 0.86; 95% CI 0.74-0.99), Odoribactergenus Odoribacter (OR 1.43; 95% CI 1.05-1.94), and Sutterellagenus Sutterella (OR 1.33; 95% CI 1.01-1.76) still maintain significant association with CP after FDR correction. Consistent directional effects for all analyses were observed in the supplementary methods. Subsequently, sensitivity analyses indicated the absence of heterogeneity, directional pleiotropy, or outliers concerning the causal effect of specific gut microbiota on CP (p > 0.05).
CONCLUSION
Our study demonstrated a gut microbiota-prostate axis, offering crucial data supporting the promising use of the GM as a candidate target for CP prevention, diagnosis, and treatment. There is a necessity for randomized controlled trials to validate the protective effect of the linked GM against the risk of CP, and to further investigate the underlying mechanisms involved.
PubMed: 38573543
DOI: 10.1007/s11255-024-04020-w -
The Science of the Total Environment May 2024As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH consumption...
As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 10 to 5.75 × 10 copies·g dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.
Topics: Humans; Nitrites; Lakes; Anaerobiosis; Methane; RNA, Ribosomal, 16S; Bacteria; Methanobacteriaceae; Bacteria, Anaerobic; Microbiota; Oxidation-Reduction; Nitrogen; Carbon; Denitrification
PubMed: 38556008
DOI: 10.1016/j.scitotenv.2024.172065 -
ISME Communications Jan 2024Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25...
Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes, and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1545 new [NiFe]-hydrogenase gene sequences were recovered, which considerably increased the number of sequences (1999) in a widely used database. [NiFe]-hydrogenases were highly abundant, as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 481 out of 1245 metagenome-assembled genomes. The relative abundance of microbes with hydrogenases accounted for ~50% of the entire community. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which has been associated with sulfur metabolism. "Group 3d", facilitating the interconversion of electrons between hydrogen and NAD, was the most abundant and mainly observed in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most abundant in proteomes. Two newly discovered groups of [NiFe]-hydrogenases, observed in and , further expanded diversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.
PubMed: 38500700
DOI: 10.1093/ismeco/ycae023