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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 -
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 -
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 -
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 -
Dermatology and Therapy Mar 2024Observational studies and clinical trials have supported the association between gut microbiota and psoriatic arthritis. However, the causal link between gut microbiota...
INTRODUCTION
Observational studies and clinical trials have supported the association between gut microbiota and psoriatic arthritis. However, the causal link between gut microbiota and psoriatic arthritis is still unclear.
METHODS
A two-sample bi-directional Mendelian randomization analysis was performed using the summary statistics of gut microbiota from the largest available genome-wide association study meta-analysis (n = 13,266) conducted by the MiBioGen consortium. The summary statistics of psoriatic arthritis were extracted directly from the FinnGen consortium, which consists of 3186 psoriatic arthritis patients and 24,086 controls. Sensitivity analyses were conducted to assess the validity of our findings. Enrichment analyses were used to investigate the biofunction and pathways.
RESULTS
Inverse variance weighted (IVW) estimates suggested that family Rikenellaceae (P = 0.032) and genus Ruminococcaceae UCG011 (P = 0.014) had a detrimental effect on psoriatic arthritis. We also noticed the negative association between the class Methanobacteria (P = 0.032), order Methanobacteriales (P = 0.032), family Methanobacteriaceae (P = 0.032), genus Eubacterium fissicatena group (P = 0.010), genus Methanobrevibacter (P = 0.031), and genus Butyricicoccus (P = 0.041) with psoriatic arthritis. Sensitivity analyses showed that genus Butyricicoccus had pleiotropy and heterogeneity. According to the results of reverse MR analysis, the causal effect of psoriatic arthritis was found on six taxa, respectivelyc family Clostridiaceae1, family Defluviitaleaceae, genus Butyrivibrio, genus Defluviitaleaceae UCG011, genus Clostridium sensu stricto1, and genus Ruminococcaceae UCG011.
CONCLUSION
This two-sample bidirectional Mendelian randomization analysis suggested that the gut microbiota had a causal effect on psoriatic arthritis and implied the potential role of probiotics in the management and prevention of psoriatic arthritis.
PubMed: 38451424
DOI: 10.1007/s13555-024-01121-3 -
Journal of Dairy Science Jul 2024The intestinal microbiota plays a pivotal role in digestive processes and maintains gut health and intestinal homeostasis. These functions may be compromised by...
Heat stress and feeding effects on the mucosa-associated and digesta microbiome and their relationship to plasma and digesta fluid metabolites in the jejunum of dairy cows.
The intestinal microbiota plays a pivotal role in digestive processes and maintains gut health and intestinal homeostasis. These functions may be compromised by increased environmental heat, which in turn reduces feed intake and gut integrity and activates the intestinal immune system. It remains unknown whether high ambient temperatures, which cause heat stress (HS) in dairy cows, disturb the eubiosis of the microbial community, and if so, to which extent the reduction in feed intake and the impairment of circulating and intestinal metabolites account for the alterations of the jejunal microbiota. To address these questions, jejunal digesta, mucosa, and plasma samples were collected from cows exposed to heat stress (HS; 28°C, temperature-humidity index [THI] = 76, n = 10), control conditions (CON; 16°C, THI = 60, n = 10), or pair-fed (PF; 16°C, THI = 60, n = 10) for 7 d. Digesta fluids were examined for pH, acetate, nonesterified fatty acids (NEFA), glucose, and lactate, and plasma samples were analyzed for glucose, lactate, BHB, triglycerides, NEFA, creatinine, and urea. The microbiota of the digesta and mucosa samples were analyzed by 16S rRNA sequencing. The α-diversity was higher in mucosa than digesta but was not affected by high ambient temperatures. However, the mucosa-associated microbiota appeared more responsive to ambient heat than the digesta microbiome. The adaptive responses under HS conditions comprised an increased mucosal abundance of Bifidobacteriaceae, Succinivibrionaceae UCG-001, Clostridia and Lactobacillus. In the digesta, HS has exerted effects on microbial abundance of Colidextribacter, and Lachnospiraceae UCG-008. Several correlations between plasma or intestinal metabolites and microbiota were elucidated, including Methanobacteriaceae correlating positively with plasma BHB and digesta glucose concentrations. Moreover, the reduction in feed intake during HS had non-negligible effects on microbial diversity and the abundance of certain taxa, underpinning the importance of nutrient supply on maintaining intestinal homeostasis.
Topics: Animals; Cattle; Female; Jejunum; Gastrointestinal Microbiome; Hot Temperature; Microbiota
PubMed: 38431250
DOI: 10.3168/jds.2023-24242 -
Frontiers in Microbiology 2024Observational studies and animal experiments suggested potential relevance between gut microbiota (GM) and cervical cancer (CC), but the relevance of this association...
BACKGROUND
Observational studies and animal experiments suggested potential relevance between gut microbiota (GM) and cervical cancer (CC), but the relevance of this association remains to be clarified.
METHODS
We performed a two-sample bidirectional Mendelian randomization (MR) analysis to explore whether there was a causal correlation between GM and CC, and the direction of causality.
RESULTS
In primary outcomes, we found that a higher abundance of and predicted higher risk of CC, and a higher abundance of and predicted lower risk of CC. During verifiable outcomes, we found that a higher abundance of and predicted a higher risk of CC, and a higher abundance of and predicted a lower risk of CC, and vice versa.
CONCLUSION
Our study implied a mutual causality between GM and CC, which provided a novel concept for the occurrence and development of CC, and might promote future functional or clinical analysis.
PubMed: 38419642
DOI: 10.3389/fmicb.2024.1336101 -
Water Research Mar 2024Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and...
Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30-50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.
Topics: Sewage; Metagenome; Anaerobiosis; Wastewater; Polysaccharides; Bioreactors; Waste Disposal, Fluid
PubMed: 38330717
DOI: 10.1016/j.watres.2024.121240 -
Synthetic and Systems Biotechnology Mar 2024Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed...
Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO is the predominant, being the genus and the species the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.
PubMed: 38292760
DOI: 10.1016/j.synbio.2023.12.007