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FEMS Microbiology Ecology Feb 2022Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some...
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8, or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Increasing formate concentrations delayed the onsets of growth and sulfate reduction of D. multivorans, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
Topics: Desulfovibrio; Formates; Microbiota; Oxidation-Reduction; Sulfates
PubMed: 35040992
DOI: 10.1093/femsec/fiac003 -
Journal of Alzheimer's Disease : JAD 2022Epidemiological studies that investigate alterations in gut microbial composition associated with cognitive dysfunction are limited.
BACKGROUND
Epidemiological studies that investigate alterations in gut microbial composition associated with cognitive dysfunction are limited.
OBJECTIVE
To examine the association between the gut microbiota and subjective memory complaints (SMCs), a self-reported, validated indicator of cognitive dysfunction.
METHODS
In this cross-sectional study of 95 older women selected from the New York University Women's Health Study (NYUWHS), we characterized the gut microbial composition using 16S rRNA gene sequencing. We estimated odds ratio (OR) from beta regression which approximates the ratio of mean relative abundances of individual bacterial taxon from phylum to genus levels by binary (2+ versus < 2) and continuous SMCs.
RESULTS
Women reporting 2 or more SMCs had higher relative abundances of genus Holdemania and family Desulfovibrionaceae compared with those reporting one or no complaint. Compared with women with < 2 SMCs, the relative abundances of Holdemania and family Desulfovibrionaceae were 2.09 times (OR: 2.09, 95% confidence interval [CI]: 1.38-3.17) and 2.10 times (OR: 2.10, 95% CI: 1.43-3.09) higher in women with 2+ SMCs, respectively (false discovery rate (FDR)-adjusted p = 0.038 and 0.010, respectively). A dose-response association was observed for genus Sutterella and family Desulfovibrionaceae. Every one-unit increase in SMCs was associated with 25% and 27% higher relative abundances of Sutterella (OR: 1.25; 95% CI: 1.11-1.40) and Desulfovibrionaceae (OR: 1.27; 95% CI: 1.13-1.42), respectively (FDR-adjusted p = 0.018 and 0.006, respectively).
CONCLUSION
Our findings support an association between alterations in the gut bacterial composition and cognitive dysfunction.
Topics: Aged; Cognitive Dysfunction; Cross-Sectional Studies; Female; Gastrointestinal Microbiome; Humans; Odds Ratio; RNA, Ribosomal, 16S
PubMed: 35570486
DOI: 10.3233/JAD-220011 -
Frontiers in Cellular and Infection... 2023Previous research has posited a potential correlation between the gut microbiota and the onset of appendicitis; however, the precise causal connection between...
BACKGROUND
Previous research has posited a potential correlation between the gut microbiota and the onset of appendicitis; however, the precise causal connection between appendicitis and the gut microbiota remains an unresolved and contentious issue.
METHODS
In this investigation, we performed a Mendelian randomization (MR) analysis employing publicly accessible summary data extracted from genome-wide association studies (GWAS) to elucidate the potential causal nexus between the gut microbiota and the development of appendicitis. We initially identified instrumental variables (IVs) through a comprehensive array of screening methodologies, subsequently executing MR analyses using the Inverse Variance Weighted (IVW) technique as our primary approach, supplemented by several alternative methods such as MR Egger, weighted median, simple mode, and weighted mode. Additionally, we implemented a series of sensitivity analysis procedures, encompassing Cochran's Q test, MR-Egger intercept test, Mendelian Randomized Polymorphism Residual and Outlier (MR-PRESSO) test, and a leave-one-out test, to affirm the robustness and validity of our findings.
RESULTS
Our investigation indicates that an elevated prevalence of Deltaproteobacteria, Christensenellaceae, Desulfovibrionaceae, Eubacterium ruminantium group, Lachnospiraceae NK4A136 group, Methanobrevibacter, Desulfovibrionales, and Euryarchaeota is inversely associated with the risk of appendicitis. Conversely, we observed a positive correlation between an increased abundance of Family XIII, Howardella, and Veillonella and the susceptibility to appendicitis. Sensitivity analyses have corroborated the robustness of these findings, and Mendelian randomization analyses provided no indications of reverse causality.
CONCLUSION
Our Mendelian randomization (MR) analysis has unveiled potential advantageous or detrimental causal associations between the gut microbiota and the occurrence of appendicitis. This study offers novel theoretical and empirical insights into the understanding of appendicitis pathogenesis, along with its implications for preventive and therapeutic strategies.
Topics: Humans; Gastrointestinal Microbiome; Appendicitis; Genome-Wide Association Study; Mendelian Randomization Analysis; Causality; Clostridiales
PubMed: 38162578
DOI: 10.3389/fcimb.2023.1320992 -
PLoS Genetics Feb 2020Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular... (Review)
Review
Many species of bacteria can manufacture materials on a finer scale than those that are synthetically made. These products are often produced within intracellular compartments that bear many hallmarks of eukaryotic organelles. One unique and elegant group of organisms is at the forefront of studies into the mechanisms of organelle formation and biomineralization. Magnetotactic bacteria (MTB) produce organelles called magnetosomes that contain nanocrystals of magnetic material, and understanding the molecular mechanisms behind magnetosome formation and biomineralization is a rich area of study. In this Review, we focus on the genetics behind the formation of magnetosomes and biomineralization. We cover the history of genetic discoveries in MTB and key insights that have been found in recent years and provide a perspective on the future of genetic studies in MTB.
Topics: Bacterial Proteins; Biomineralization; DNA Transposable Elements; Desulfovibrio; Ferrosoferric Oxide; Genes, Bacterial; Magnetosomes; Magnetospirillum; Metal Nanoparticles; Mutagenesis; Mutation
PubMed: 32053597
DOI: 10.1371/journal.pgen.1008499 -
Frontiers in Microbiology 2022Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized...
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera ( and ) and one former invalid genus ("") were officially proposed. Further, by applying the 95-96% average nucleotide identity (ANI) standard and the 70% digital DNA-DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes analysis, it was confirmed that most strains display metal tolerance.
PubMed: 35694308
DOI: 10.3389/fmicb.2022.738205 -
Nature Communications Apr 2024The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large...
The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.
Topics: Humans; Female; Gastrointestinal Microbiome; Middle Aged; Diverticulitis; Feces; Aged; Prospective Studies; Bilophila; Metabolomics; Case-Control Studies; Clostridiales; Bile Acids and Salts; Adult; Dietary Fiber; Metabolome; Metagenomics
PubMed: 38684664
DOI: 10.1038/s41467-024-47859-4 -
Molecules (Basel, Switzerland) May 2023A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to... (Review)
Review
A story going back almost 40 years is presented in this manuscript. This is a different and more challenging way of reporting my research and I hope it will be useful to and target a wide-ranging audience. When preparing the manuscript and collecting references on the subject of this paper-aldehyde oxidoreductase from -I felt like I was travelling back in time (and space), bringing together the people that have contributed most to this area of research. I sincerely hope that I can give my collaborators the credit they deserve. This study is not presented as a chronologic narrative but as a grouping of topics, the development of which occurred over many years.
Topics: Humans; Aldehyde Oxidoreductases; Desulfovibrio gigas; Desulfovibrio; Molybdenum; Aldehyde Dehydrogenase
PubMed: 37241969
DOI: 10.3390/molecules28104229 -
Dietary Plant and Animal Protein Sources Oppositely Modulate Fecal and in Vegetarians and Omnivores.Microbiology Spectrum Apr 2022The food we eat not only nourishes our bodies but also provides nutrients to the bacteria living in our guts. Gut bacterial communities are known to be affected by many...
The food we eat not only nourishes our bodies but also provides nutrients to the bacteria living in our guts. Gut bacterial communities are known to be affected by many factors, including diet and bowel cleansing, but the impacts of vegetarian and omnivore diets on fecal bacterial composition are still uncertain. In this study, we analyzed the bacterial compositions of fecal samples from vegetarians and omnivores 5 to 7 days after bowel cleansing, and we correlated specific dietary constituents with the relative abundances of specialized fecal bacteria. A total of 46 participants (23 vegetarians and 23 omnivores) were recruited. All participants underwent standard bowel cleansing before colonoscopy screening. Fecal samples were collected from each participant 5 to 7 days after bowel cleansing, and the fecal microbiota compositions were analyzed with next-generation sequencing. Sixteen participants also provided an image-based dietary record for nutritional assessment. No major differences between dietary groups were observed in terms of fecal bacterial richness, alpha diversity, or beta diversity. A minority of potential pathobionts tended to be elevated in omnivores compared to vegetarians, whereas potential probiotic species tended to be higher in the vegetarians. Detailed dietary assessments further revealed that the plant- and animal-derived proteins may oppositely modulate the relative abundances of pathobionts Bilophila and Lachnoclostridium. However, these results were not statistically significant after multiple-comparison correction. These results suggest that specialized probiotic and pathobiont microbiota constituents are sensitive to the plant- or animal-derived dietary components ingested by vegetarians and omnivores after bowel cleansing. Dietary pattern and food choice are associated with expansion of gut pathobionts and risk for metabolic and colonic disease. However, the effects of dietary interventions on intestinal microbiota remain unclear. After bowel cleansing, potential pathobionts and probiotic bacteria were increased in omnivores and vegetarians, respectively. The pathobionts Bilophila and Lachnoclostridium were oppositely modulated by dietary animal and plant protein. From a clinical perspective, fecal pathobionts that may indicate risk for metabolic and colonic disease can potentially be modulated with dietary interventions.
Topics: Animals; Bacteria; Bilophila; Clostridiales; Colonic Diseases; Diet; Feces; Humans; Vegetarians
PubMed: 35285706
DOI: 10.1128/spectrum.02047-21 -
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 -
Parasites, Hosts and Diseases Feb 2023The genus Babesia includes parasites that can induce human and animal babesiosis, which are common in tropical and subtropical regions of the world. The gut microbiota...
The genus Babesia includes parasites that can induce human and animal babesiosis, which are common in tropical and subtropical regions of the world. The gut microbiota has not been examined in hamsters infected by Babesia duncani. Red blood cells infected with B. duncani were injected into hamsters through intraperitoneal route. To evaluate the changes in gut microbiota, DNAs were extracted from small intestinal contents, acquired from hamsters during disease development. Then, the V4 region of the 16S rRNA gene of bacteria was sequenced using the Illumina sequencing platform. Gut microbiota alternation and composition were assessed according to the sequencing data, which were clustered with >97.0% sequence similarity to create amplicon sequence variants (ASVs). Bacteroidetes and Firmicutes were made up of the major components of the gut microbiota in all samples. The abundance of Bacteroidetes elevated after B. duncani infection than the B. duncani-free group, while Firmicutes and Desulfobacterota declined. Alpha diversity analysis demonstrated that the shown ASVs were substantially decreased in the highest parasitemia group than B. duncani-free and lower parasitemia groups. Potential biomarkers were discovered by Linear discriminant analysis Effect Size (LEfSe) analysis, which demonstrated that several bacterial families (including Muribaculaceae, Desulfovibrionaceae, Oscillospiraceae, Helicobacteraceae, Clostridia UGG014, Desulfovibrionaceae, and Lachnospiraceae) were potential biomarkers in B. duncani-infected hamsters. This research demonstrated that B. duncani infectious can modify the gut microbiota of hamsters.
Topics: Animals; Cricetinae; Humans; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Parasitemia; Babesia; Bacteria; Firmicutes; Bacteroidetes; Biomarkers
PubMed: 37170463
DOI: 10.3347/PHD.22142