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New Microbes and New Infections Jun 2024
PubMed: 38799975
DOI: 10.1016/j.nmni.2024.101409 -
New Microbes and New Infections Jun 2024
Expression of Concern: Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women.
PubMed: 38799966
DOI: 10.1016/j.nmni.2024.101259 -
New Microbes and New Infections Jun 2024
PubMed: 38799819
DOI: 10.1016/j.nmni.2024.101408 -
Genes Jun 2023Infertility incidence is rising worldwide, with male infertility accounting for about 50% of cases. To date, several factors have been associated with male infertility;...
Infertility incidence is rising worldwide, with male infertility accounting for about 50% of cases. To date, several factors have been associated with male infertility; in particular, it has been suggested that semen microbiota may play a role. Here, we report the NGS-based analyses of 20 semen samples collected from men with (Case) and without (Control) semen alterations. Genomic DNA was extracted from each collected sample, and a specific PCR was carried out to amplify the V4-V6 regions of the 16S rRNA. Sequence reactions were carried out on the MiSeq and analyzed by specific bioinformatic tools. We found a reduced richness and evenness in the Case versus the Control group. Moreover, specific genera, the , the and the were significantly increased in the Case compared to the Control group. Finally, we highlighted a correlation between the microbial profile and semen hyperviscosity. Even if further studies are required on larger groups of subjects to confirm these findings and explore mechanistic hypotheses, our results confirm the correlation between semen features and seminal microbiota. These data, in turn, may open the way to the possible use of semen microbiota as an attractive target for developing novel strategies for infertility management.
Topics: Humans; Male; Semen; Metagenomics; RNA, Ribosomal, 16S; Infertility, Male; Semen Analysis
PubMed: 37372408
DOI: 10.3390/genes14061228 -
Nutrients Feb 2023Protein-energy malnutrition still impacts children's growth and development. We investigated the prolonged effects of egg supplementation on growth and microbiota in... (Randomized Controlled Trial)
Randomized Controlled Trial
Protein-energy malnutrition still impacts children's growth and development. We investigated the prolonged effects of egg supplementation on growth and microbiota in primary school children. For this study, 8-14-year-old students (51.5% F) in six rural schools in Thailand were randomly assigned into three groups: (1) whole egg (WE), consuming 10 additional eggs/week ( = 238) ( = 238); (2) protein substitute (PS), consuming yolk-free egg substitutes equivalent to 10 eggs/week ( = 200); and (3) control group (C, ( = 197)). The outcomes were measured at week 0, 14, and 35. At the baseline, 17% of the students were underweight, 18% were stunted, and 13% were wasted. At week 35, compared to the C group the weight and height difference increased significantly in the WE group (3.6 ± 23.5 kg, < 0.001; 5.1 ± 23.2 cm, < 0.001). No significant differences in weight or height were observed between the PS and C groups. Significant decreases in atherogenic lipoproteins were observed in the WE, but not in PS group. HDL-cholesterol tended to increase in the WE group (0.02 ± 0.59 mmol/L, ). The bacterial diversity was similar among the groups. The relative abundance of increased by 1.28-fold in the WE group compared to the baseline and differential abundance analysis which indicated that increased and decreased significantly. In conclusion, prolonged whole egg supplementation is an effective intervention to improve growth, nutritional biomarkers, and gut microbiota with unaltered adverse effects on blood lipoproteins.
Topics: Adolescent; Child; Humans; Body Weight; Dietary Supplements; Eggs; Gastrointestinal Microbiome; Lipoproteins
PubMed: 36904143
DOI: 10.3390/nu15051143 -
BioMed Research International 2022The relationship between urinary system tumors and urothelial microorganisms remains unexplored. This study is aimed at exploring the relationship between urinary flora...
The relationship between urinary system tumors and urothelial microorganisms remains unexplored. This study is aimed at exploring the relationship between urinary flora and urinary tumors and identifying potential biomarkers for urinary tumors and new targets for prevention. We included four healthy adults (control group) and six patients diagnosed with urinary tract tumors (tumor group). In both groups, 10 and 50 ml clean middle urine samples were reserved. The 10 ml samples were analyzed (including pH, specific gravity, and leukocytes) using an automatic urine analyzer, and the 50 ml samples were analyzed by DNA extraction, 16S rRNA gene amplification, and high-throughput sequencing. The correlation between routine urine analysis and sequencing results was also analyzed. Testing using the DESeq2 method showed that, at the order level, there were significant differences in the abundance of Caulobacterales between the urinary flora of the two groups ( < 0.05); family level, , , and ( < 0.05); genus level, , , , , , , and ( < 0.05). LEfSe analysis found specific bacteria at the genus level in the urinary flora of the tumor group, namely, (genus Digestiflora) ( < 0.001) and Varibaculum ( < 0.001). Further correlation analysis showed that both species were positively correlated with the urine pH ( < 0.05). PICRUSt analysis showed significant differences in the two functional pathways of cell transformation and metabolism ( < 0.05). Combined with the results of bioinformatics analysis, some differential bacteria may be new biomarkers for urologic tumors, and there may be a correlation between urine pH and tumor occurrence. However, large-scale prospective studies and in vitro and in vivo experiments are required to further test and verify these findings.
Topics: Actinomycetaceae; Adult; Bacteria; Clostridiales; Humans; Prospective Studies; RNA, Ribosomal, 16S; Urinary Tract; Urologic Neoplasms
PubMed: 35872872
DOI: 10.1155/2022/9368687 -
European Urology Oncology Aug 2022Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been reported.
OBJECTIVE
To provide improved characterisation of the prostate and urine microbiome and to investigate the prognostic potential of the bacteria present.
DESIGN, SETTING, AND PARTICIPANTS
Microbiome profiles were interrogated in sample collections of patient urine (sediment microscopy: n = 318, 16S ribosomal amplicon sequencing: n = 46; and extracellular vesicle RNA-seq: n = 40) and cancer tissue (n = 204).
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS
Microbiomes were assessed using anaerobic culture, population-level 16S analysis, RNA-seq, and whole genome DNA sequencing.
RESULTS AND LIMITATIONS
We demonstrate an association between the presence of bacteria in urine sediments and higher D'Amico risk prostate cancer (discovery, n = 215 patients, p < 0.001; validation, n = 103, p < 0.001, χ test for trend). Characterisation of the bacterial community led to the (1) identification of four novel bacteria (Porphyromonas sp. nov., Varibaculum sp. nov., Peptoniphilus sp. nov., and Fenollaria sp. nov.) that were frequently found in patient urine, and (2) definition of a patient subgroup associated with metastasis development (p = 0.015, log-rank test). The presence of five specific anaerobic genera, which includes three of the novel isolates, was associated with cancer risk group, in urine sediment (p = 0.045, log-rank test), urine extracellular vesicles (p = 0.039), and cancer tissue (p = 0.035), with a meta-analysis hazard ratio for disease progression of 2.60 (95% confidence interval: 1.39-4.85; p = 0.003; Cox regression). A limitation is that functional links to cancer development are not yet established.
CONCLUSIONS
This study characterises prostate and urine microbiomes, and indicates that specific anaerobic bacteria genera have prognostic potential.
PATIENT SUMMARY
In this study, we investigated the presence of bacteria in patient urine and the prostate. We identified four novel bacteria and suggest a potential prognostic utility for the microbiome in prostate cancer.
Topics: Bacteria; Humans; Male; Microbiota; Prostate; Prostatic Neoplasms; RNA, Ribosomal, 16S
PubMed: 35450835
DOI: 10.1016/j.euo.2022.03.006 -
Microbial Ecology May 2023Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt...
Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.
Topics: Animals; Humans; Trichomonas; Eagles; Europe
PubMed: 35385973
DOI: 10.1007/s00248-022-02002-y -
New Microbes and New Infections Nov 2019sp. nov. strain Marseille-P2802 (= CSUR P2802 = DSM 103074) is a new species within the genus in the phylum Actinobacteria that was isolated from the urine of a...
sp. nov. strain Marseille-P2802 (= CSUR P2802 = DSM 103074) is a new species within the genus in the phylum Actinobacteria that was isolated from the urine of a 59-year-old man treated with chronic haemodialysis for diabetic nephropathy.
PubMed: 31641508
DOI: 10.1016/j.nmni.2019.100591 -
New Microbes and New Infections Sep 2019Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight...
Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: sp. nov. strain Marseille-P5647, sp. nov. strain Marseille-P5644 and sp. nov. strain Marseille-P5995, which we describe according to the concept of taxonogenomics.
PubMed: 31367386
DOI: 10.1016/j.nmni.2019.100585