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BMC Medical Genomics Jan 2024Dysbacteriosis of intestinal tract may cause systemic inflammation, making distant anatomical locations more susceptible to illness. Recent research has demonstrated...
BACKGROUND
Dysbacteriosis of intestinal tract may cause systemic inflammation, making distant anatomical locations more susceptible to illness. Recent research has demonstrated that the microbiome can affect both prostatitis and the inflammation of the prostate that is linked to prostate cancer. It is still unclear, though, whether this relationship indicates causation. We conducted a Mendelian randomization investigation on two samples to fully uncover gut microbiota's potential genetic causal role in prostatitis.
METHOD
Prostatitis (1859 prostatitis cases and 72,799 controls) was utilized as the outcome, while SNPs highly linked with 196 microbial taxa (18 340 people) were chosen as instrumental factors. Random effects, inverse variance weighting, weighted medians, and MR-Egger were used to analyze causal effects. The Cochran's Q test, funnel plot, leave-one-out analysis, and MR-Egger intercept test were all used in the sensitivity analysis.
RESULTS
A causal effect in lowering the incidence of prostatitis is anticipated for five gut microorganisms (Methanobacteria, Methanobacteriaceae, Erysipelatoclostridium, Parasutterella, and Slackia; P < 0.05). Four gut bacteria, including Faecalibacterium, LachnospiraceaeUCG004, Sutterella, and Gastranaerophilales, are predicted to play a causal role in increasing the risk of prostatitis (P < 0.05). There were no discernible estimates of pleiotropy or heterogeneity.
CONCLUSION
Our investigation established the genetic links between nine gut microorganisms and prostatitis, which may offer fresh perspectives and a theoretical framework for the future prevention and management of prostatitis.
Topics: Male; Humans; Prostatitis; Gastrointestinal Microbiome; Inflammation; Nonoxynol; Polymorphism, Single Nucleotide; Genome-Wide Association Study
PubMed: 38273299
DOI: 10.1186/s12920-024-01812-y -
Cancers Dec 2023Progressive intestinal mucosal damage occurs over years prior to colorectal cancer (CRC) development. The endoscopic screening of polyps and histopathological...
Progressive intestinal mucosal damage occurs over years prior to colorectal cancer (CRC) development. The endoscopic screening of polyps and histopathological examination are used clinically to determine the risk and progression of mucosal lesions. We analyzed fecal microbiota compositions using 16S rRNA gene-based metataxonomic analyses and the levels of short-chain fatty acids (SCFAs) using gas chromatography in volunteers undergoing colonoscopy and histopathological analyses to determine the microbiota shifts occurring at the early stages of intestinal mucosa alterations. The results were compared between diagnosis groups (nonpathological controls and polyps), between samples from individuals with hyperplastic polyps or conventional adenomas, and between grades of dysplasia in conventional adenomas. Some microbial taxa from the and phyla were the most affected when comparing the diagnosis and histopathological groups. Deeper microbiota alterations were found in the conventional adenomas than in the hyperplastic polyps. The group was enriched in both the hyperplastic polyps and conventional adenomas, whereas the family was enriched only in the hyperplastic polyps. The abundance of , , , , , , and shifted in conventional adenomas depending on the grade of dysplasia, without affecting the major SCFAs. Our results suggest a reorganization of microbial consortia involved in gut fermentative processes.
PubMed: 38201530
DOI: 10.3390/cancers16010104 -
Microbiology Spectrum Feb 2024was the sole representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases,...
was the sole representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated species. Here, a novel species, Methanosphaera massiliense (. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. . M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of . M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of in human microbiota, questions the zoonotic sources of . M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which was the only cultivated representative. We grew Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected . M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
Topics: Humans; Animals; Swine; Macropodidae; Methanobacteriaceae; Methane; Feces; Hydrogen; Ethanol; Phylogeny; RNA, Ribosomal, 16S
PubMed: 38189277
DOI: 10.1128/spectrum.05141-22 -
Frontiers in Microbiology 2023Some observational studies have shown that immune thrombocytopenia (ITP) is highly associated with the alteration-composition of gut microbiota. However, the causality...
BACKGROUND
Some observational studies have shown that immune thrombocytopenia (ITP) is highly associated with the alteration-composition of gut microbiota. However, the causality of gut microbiota on ITP has not yet been determined.
METHODS
Based on accessible summary statistics of the genome-wide union, the latent connection between ITP and gut microbiota was estimated using bi-directional Mendelian randomization (MR) and multivariable MR (MVMR) analyses. Inverse variance weighted (IVW), weighted median analyses, and MR-Egger regression methods were performed to examine the causal correlation between ITP and the gut microbiota. Several sensitivity analyses verified the MR results. The strength of causal relationships was evaluated using the MR-Steiger test. MVMR analysis was undertaken to test the independent causal effect. MR analyses of reverse direction were made to exclude the potential of reverse correlations. Finally, GO enrichment analyses were carried out to explore the biological functions.
RESULTS
After FDR adjustment, two microbial taxa were identified to be causally associated with ITP ( < 0.10), namely ( = 7.31 × 10) and ( = 7.31 × 10). In addition, eight microbial taxa were considered as potentially causal features under the nominal significance ( < 0.05): , , , , , , , and . According to the reverse-direction MR study findings, the gut microbiota was not significantly affected by ITP. There was no discernible horizontal pleiotropy or instrument heterogeneity. Finally, GO enrichment analyses showed how the identified microbial taxa participate in ITP through their underlying biological mechanisms.
CONCLUSION
Several microbial taxa were discovered to be causally linked to ITP in this MR investigation. The findings improve our understanding of the gut microbiome in the risk of ITP.
PubMed: 38075905
DOI: 10.3389/fmicb.2023.1190866 -
Scientific Reports Dec 2023The human gut microbiota is a complex ecosystem that affects a range of human physiology. In order to explore the dynamics of the human gut microbiota, we used a system...
The human gut microbiota is a complex ecosystem that affects a range of human physiology. In order to explore the dynamics of the human gut microbiota, we used a system of ordinary differential equations to model mathematically the biomass of three microorganism populations: Bacteroides thetaiotaomicron, Eubacterium rectale, and Methanobrevibacter smithii. Additionally, we modeled the concentrations of relevant nutrients necessary to sustain these populations over time. Our model highlights the interactions and the competition among these three species. These three microorganisms were specifically chosen due to the system's end product, butyrate, which is a short chain fatty acid that aids in developing and maintaining the intestinal barrier in the human gut. The basis of our mathematical model assumes the gut is structured such that bacteria and nutrients exit the gut at a rate proportional to its volume, the rate of volumetric flow, and the biomass or concentration of the particular population or nutrient. We performed global sensitivity analyses using Sobol' sensitivities to estimate the relative importance of model parameters on simulation results.
Topics: Humans; Bacteroides thetaiotaomicron; Eubacterium; Methanobrevibacter; Ecosystem; Bacteroides; Models, Theoretical
PubMed: 38040895
DOI: 10.1038/s41598-023-48524-4 -
New Biotechnology Mar 2024Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore,...
Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.
Topics: Humans; Oil and Gas Fields; Anthropogenic Effects; Bacteria; Microbiota; Water; Disinfectants
PubMed: 38040289
DOI: 10.1016/j.nbt.2023.11.004 -
Zhong Nan Da Xue Xue Bao. Yi Xue Ban =... Aug 2023The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear....
OBJECTIVES
The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable characteristics of intestinal flora between patients simply with CI and CI-T2DM.
METHODS
This study retrospectively collected the patients who were admitted to the Affiliated Hospital of Putian University from September 2021 to September 2022. The patients were divided into a CI group (=12) and a CI-T2DM group (=12). Simultaneously, 12 healthy people were selected as a control group. Total DNA was extracted from feces specimens. Illumina Novaseq sequencing platform was used for metagenomic sequencing. The Knead Data software, Kraken2 software, and Bracken software were applied for sequencing analysis.
RESULTS
At phylum level, the average ratio of Firmicutes, Bacteroidetes, and Proteobacteria in the CI-T2DM group were 33.07%, 54.80%, and 7.00%, respectively. In the CI group, the ratios of each were 14.03%, 69.62%, and 11.13%, respectively, while in the control group, the ratios were 50.99%, 37.67%, and 5.24%, respectively. There was significant differences in the distribution of Firmicutes (=6.130, =0.011) among the 3 groups. At the family level, compared with the CI group, the relative abundance of Eubacteriaceae (=8.062, <0.001) in the CI-T2DM group was significantly increased, while Corynebacteriaceae (=4.471, <0.001), Methanobacteriaceae (=3.406, =0.003), and Pseudomonadaceae (=2.352, =0.028) were decreased significantly. At the genus level, compared with the CI group, there was a relative abundance of (=6.242, <0.001), (=8.448, <0.001), and (=3.442, =0.002) in the CI-T2DM group which was significantly increased. In terms of (=3.466, =0.002), (=2.846, =0.009) and (=2.352, =0.028), their distributions were decreased significantly in the CI-T2DM group. At the species level, compared with the CI group, the relative abundance of (=6.242, <0.001) in the CI-T2DM group was significantly increased, while (=2.352, =0.028) was decreased significantly. Still at the genus level, linear discriminant analysis effect size (LEfSe) analysis showed that the distributions of and were determined to be the most significantly different between the CI-T2DM and the CI group. At the species level, the total number of operational taxonomic units (OTUs) in the 3 groups was 1 491. There were 169, 221, and 192 kinds of OTUs unique to the CI-T2DM, CI, and control group, respectively.
CONCLUSIONS
From phylum level to species level, the composition of intestinal flora in the patients with CI-T2DM is different from those in the patients simply with CI. The change in the proportion of , and compared with the healthy population is an important feature of intestinal flora imbalance in the patients with CI and with CI-T2DM. Attention should be paid to the differential distribution of and butyrate producing bacteria.
Topics: Humans; Gastrointestinal Microbiome; Diabetes Mellitus, Type 2; Retrospective Studies; Bacteria; High-Throughput Nucleotide Sequencing
PubMed: 37875356
DOI: 10.11817/j.issn.1672-7347.2023.220558 -
Clinical and Experimental Rheumatology Jan 2024To assess whether there is a bidirectional causal relationship between the composition of gut microbiota and rheumatoid arthritis (RA), and to identify specific...
OBJECTIVES
To assess whether there is a bidirectional causal relationship between the composition of gut microbiota and rheumatoid arthritis (RA), and to identify specific pathogenic bacterial taxa via the Mendelian randomisation (MR) analysis.
METHODS
We acquired single nucleotide polymorphisms (SNPs) associated with the composition of gut microbiota (n=18,340) and with RA (n=331,313) from publicly available genome-wide association studies (GWAS). The genome-wide threshold was 1 × 10-5 in the forward MR analysis and was 5 × 10-8 in the reverse MR analysis. Inverse variance weighted (IVW) was the main method to analyse causality, and MR results were verified by several sensitivity analyses including weighted median, MR Egger, and MR Pleiotropy Residual Sum and Outlier (PRESSO).
RESULTS
The IVW method suggested that eight taxa were positively correlated with RA, including: MollicutesRF9 (pIVW <0.01), Alphaproteobacteria (pIVW <0.01), Betaproteobacteria (p IVW =0.04), Bacteroidaceae (pIVW <0.01), Adlercreutzia (pIVW <0.01), Bacteroides (pIVW <0.01), Butyricimonas (p IVW =0.03) and Holdemanella (pIVW =0.03). Six bacterial taxa were negatively correlated with RA, including Desulfovibrionales (pIVW = 0.01), Methanobacteriales (pIVW <0.01), Methanobacteria (PIVW <0.01), Desulfovibrionaceae (pIVW <0.01), Methanobacteriaceae (pIVW <0.01) and Butyrivibrio (pIVW =0.02). Heterogeneity (p>0.05) and pleiotropy (p>0.05) analysis confirmed the robustness of the MR results.
CONCLUSIONS
We identified some specific bacterial taxa that were causally associated with the risk of RA, providing new insights into prevention and diagnosis of RA.
Topics: Humans; Gastrointestinal Microbiome; Genome-Wide Association Study; Arthritis, Rheumatoid; Polymorphism, Single Nucleotide
PubMed: 37812479
DOI: 10.55563/clinexprheumatol/p9ig7c -
ACS Omega Sep 2023Developing novel strategies to enhance volatile fatty acid (VFA) yield from abundant waste resources is imperative to improve the competitiveness of biobased VFAs over...
Developing novel strategies to enhance volatile fatty acid (VFA) yield from abundant waste resources is imperative to improve the competitiveness of biobased VFAs over petrochemical-based VFAs. This study hypothesized to improve the VFA yield from food waste via three strategies, viz., pH adjustment (5 and 10), supplementation of selenium (Se) oxyanions, and heat treatment of the inoculum (at 85 °C for 1 h). The highest VFA yield of 0.516 g COD/g VS was achieved at alkaline pH, which was 45% higher than the maximum VFA production at acidic pH. Heat treatment resulted in VFA accumulation after day 10 upon alkaline pretreatment. Se oxyanions acted as chemical inhibitors to improve the VFA yield at pH 10 with non-heat-treated inoculum (NHT). Acetic and propionic acid production was dominant at alkaline pH (NHT); however, the VFA composition diversified under the other tested conditions. More than 95% Se removal was achieved on day 1 under all the conditions tested. However, the heat treatment was detrimental for selenate reduction, with less than 15% Se removal after 20 days. Biosynthesized Se nanoparticles were confirmed by transmission and scanning electron microscopy and and energy dispersive X-ray analyses. The heat treatment inhibited the presence of nonsporulating bacteria and methanogenic archaea (). High-throughput sequencing also revealed higher relative abundances of the bacterial families (such as , , and ) that are capable of VFA production and/or selenium reduction.
PubMed: 37779932
DOI: 10.1021/acsomega.2c06459 -
Antioxidants (Basel, Switzerland) Sep 2023This study aimed to investigate the effects of dietary tannic acid (TAN) on the gas production, growth performance, antioxidant capacity, rumen microflora, and...
Dietary Supplementation of Tannic Acid Promotes Performance of Beef Cattle via Alleviating Liver Lipid Peroxidation and Improving Glucose Metabolism and Rumen Fermentation.
This study aimed to investigate the effects of dietary tannic acid (TAN) on the gas production, growth performance, antioxidant capacity, rumen microflora, and fermentation function of beef cattle through in vitro and in vivo experiments. TAN was evaluated at 0.15% (dry matter basis, DM) in the in vitro experiment and 0.20% (DM basis) in the animal feeding experiment. The in vitro results revealed that compared with control (CON, basal diet without TAN), the addition of TAN significantly increased the cumulative gas production and asymptotic gas production per 0.20 g dry matter substrate ( < 0.01), with a tendency to reduce methane concentration after 96 h of fermentation ( = 0.10). Furthermore, TAN supplementation significantly suppressed the relative abundance of and in the fermentation fluid (LDA > 2.50, < 0.05). The in vivo experiment showed that compared with CON, the dietary TAN significantly improved average daily gain (+0.15 kg/d), dressing percent (+1.30%), net meat percentage (+1.60%), and serum glucose concentration (+23.35%) of beef cattle ( < 0.05), while it also significantly reduced hepatic malondialdehyde contents by 25.69% ( = 0.02). Moreover, the TAN group showed significantly higher alpha diversity ( < 0.05) and increased relative abundance of and (LDA > 2.50, < 0.05), while the relative abundance of in rumen microbial community was significantly decreased ( < 0.05) as compared to that of the CON group. In conclusion, the dietary supplementation of TAN could improve the growth and slaughter performance and health status of beef cattle, and these favorable effects might be attributed to its ability to alleviate liver lipid peroxidation, enhance glucose metabolism, and promote a balanced rumen microbiota for optimal fermentation.
PubMed: 37760076
DOI: 10.3390/antiox12091774