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Frontiers in Cell and Developmental... 2022The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was...
The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was shown to be related to sperm quality parameters, suggesting an effect in human fertility and postulating it as a biomarker candidate. However, its relationship to sperm DNA integrity has not been studied yet. The aim of the present study is to characterize the seminal microbiota of a western Mediterranean population and to evaluate its relationship to sperm chromatin integrity parameters, and oxidative stress. For that purpose, 14 samples from sperm donors and 42 samples from infertile idiopathic patients were obtained and were analyzed to assess the composition of the microbiota through full-length gene sequencing (Illumina MiSeq platform). Microbial diversity and relative abundances were compared to classic sperm quality parameters (macroscopic semen parameters, motility, morphology and concentration), chromatin integrity (global DNA damage, double-stranded DNA breaks and DNA protamination status) and oxidative stress levels (oxidation-reduction potential). The seminal microbiota observed of these samples belonged to the phyla , , and . The most abundant genera were , , , , , , , , , and . To our knowledge, this is the first detection of genus in seminal samples. Two clusters of microbial profiles were built based on a clustering analysis, and specific genera were found with different frequencies in relation to seminal quality defects. The abundances of several bacteria negatively correlate with the sperm global DNA fragmentation, most notably , and . The latter two were also associated with higher sperm motility and additionally with lower oxidative-reduction potential. , and correlated with reduced chromatin protamination status and increased double-stranded DNA fragmentation. These effects on DNA integrity coincide in many cases with the metabolism or enzymatic activities of these genera. Significant differences between fertile and infertile men were found in the relative presence of the family and the , and genera, which supports its possible involvement in male fertility. Our findings sustain the hypothesis that the seminal microbiome has an effect on male fertility.
PubMed: 35837328
DOI: 10.3389/fcell.2022.937157 -
Anaerobe Jun 2022Gram-positive anaerobic cocci (GPAC) are often regarded as harmless commensals associated with skin and mucosal surfaces. Investigations regarding these bacterial...
OBJECTIVES
Gram-positive anaerobic cocci (GPAC) are often regarded as harmless commensals associated with skin and mucosal surfaces. Investigations regarding these bacterial species often concern clinical case reports. In immunocompromised individuals, in the presence of comorbidities, such as diabetes or due to breach of skin barriers, the GPAC can cause infections. Nonetheless, information on the direct impact of these bacteria on blood-derived immune cells remains sparse.
METHODS
Heat-inactivated GPAC strains (Finegoldia magna, Peptoniphilus harei, Parvimonas micra and Anaerococcus spp.) were incubated with whole blood from healthy human donors for 15 min or 4 h. Following the incubation, plasma samples were collected and analysed by ELISA for secretion of heparin-binding protein (HBP), myeloperoxidase (MPO), calprotectin (S100A8/S100A9; MRP-8/MRP-14) and TNFα as markers for immune cell activation.
RESULTS
The direct interaction of GPAC with whole blood demonstrated a significant effect on the immune response. Incubation of the bacterial strains with blood triggered rapid secretion of sepsis markers HBP and calprotectin, as well as the pro-inflammatory cytokine TNFα. Due to lack of MPO secretion at the early time point, it was hypothesised that the early HBP originated from the neutrophil secretory vesicles. Trypsin-treatment of the bacteria slightly reduced the HBP release, suggesting an involvement of bacterial surface proteins.
CONCLUSIONS
The findings suggest that GPAC species isolated from blood might pose an underestimated threat to the host. Further research concerning anaerobic cocci in direct interaction with the human host is therefore needed and justified.
Topics: Anaerobiosis; Antimicrobial Cationic Peptides; Bacteria, Anaerobic; Blood Proteins; Gram-Positive Cocci; Humans; Leukocyte L1 Antigen Complex; Sepsis; Tumor Necrosis Factor-alpha
PubMed: 35545182
DOI: 10.1016/j.anaerobe.2022.102584 -
Scientific Reports Apr 2022The potential impact of the composition of maternal breast milk is poorly known in children who develop celiac disease (CD). The aim of our study was to compare the...
The potential impact of the composition of maternal breast milk is poorly known in children who develop celiac disease (CD). The aim of our study was to compare the microbiota composition and the concentrations of immune markers in breast milk from mothers whose offspring carried the genetic predisposition to CD, and whether they did or did not develop CD during follow-up for the first 3 years of life. Maternal breast milk samples [CD children (n = 6) and healthy children (n = 18)] were collected 3 months after delivery. Enzyme-linked immunosorbent assays were used to measure TGF-β1, TGF-β2, sIgA, MFG-E8 and sCD14. For microbiota analysis, next generation (Illumina) sequencing, real-time PCR and denaturing gradient gel electrophoresis were used. Phylotype abundance and the Shannon 'H' diversity index were significantly higher in breast milk samples in the CD group. There was higher prevalence of the phyla Bacteroidetes and Fusobacteria, the classes Clostridia and Fusobacteriia, and the genera Leptotrichia, Anaerococcus, Sphingomonas, Actynomyces and Akkermansia in the CD group. The immunological markers were differently associated with some Gram-negative bacterial genera and species (Chryseobacterium, Sphingobium) as well as Gram-positive species (Lactobacillus reuteri, Bifidobacterium animalis). In conclusion, the microbiota in breast milk from mothers of genetically predisposed offspring who presented CD showed a higher bacterial phylotype abundance and diversity, as well as a different bacterial composition, as compared with the mothers of unaffected offspring. These immune markers showed some associations with bacterial composition and may influence the risk for development of CD beyond early childhood.
Topics: Bacteria; Celiac Disease; Child; Child, Preschool; Female; Humans; Limosilactobacillus reuteri; Lipopolysaccharide Receptors; Microbiota; Milk, Human
PubMed: 35459889
DOI: 10.1038/s41598-022-10679-x -
Pathogens (Basel, Switzerland) Apr 2022Deciphering the interactions between ticks and their microbiome is key to revealing new insights on tick biology and pathogen transmission. However, knowledge on...
Deciphering the interactions between ticks and their microbiome is key to revealing new insights on tick biology and pathogen transmission. However, knowledge on tick-borne microbiome diversity and their contribution to drug resistance is scarce in sub-Saharan Africa (SSA), despite endemism of ticks. In this study, high-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used to characterize the bacterial community structure and associated antibiotic resistance markers in , and ticks infesting Nguni cattle ( spp.). Twenty-one (seven families and fourteen genera) potentially pathogenic and endosymbiotic bacterial taxa were differentially enriched in two tick genera. In ticks, a higher abundance of (35.6%), (14.4%), (11.1%) (3.7%), and (4.7%) was detected. However, (38.6%), (7%), and (2%) were the major differentially abundant taxa in . and . Further, an abundance of 50 distinct antibiotic resistance biomarkers relating to multidrug resistance (MDR) efflux pumps, drug detoxification enzymes, ribosomal protection proteins, and secretion systems, were inferred in the microbiome. This study provides theoretical insights on the microbiome and associated antibiotic resistance markers, important for the design of effective therapeutic and control decisions for tick-borne diseases in the SSA region.
PubMed: 35456107
DOI: 10.3390/pathogens11040432 -
Frontiers in Cell and Developmental... 2022Vulvar lichen sclerosus (VLS) is a chronic inflammatory skin disease that brings life-long and psychological distress to patients. It remains unclear whether this...
Vulvar lichen sclerosus (VLS) is a chronic inflammatory skin disease that brings life-long and psychological distress to patients. It remains unclear whether this condition is related to changes in the skin microbial community. The aim of this study was to evaluate the compositional characteristics of the vulvar skin microbiota between VLS patients and asymptomatic postmenopausal women. We included 60 cases of postmenopausal patients in the outpatient vulvar clinic of Peking University First Hospital from August 2020 to October 2020. Thirty-one patients were diagnosed with VLS by vulvar skin biopsy (VLS group), while 29 women were asymptomatic volunteers (control group). DNA was extracted from vulvar skin swabs of the VLS and control groups. The V3-V4 fragments of 16S rRNA were targeted for high-throughput sequencing and gene sequence analysis. The sequencing results were analysed by diversity, diversity, species composition, LEfSe analysis to compare the compositional differences of the vulvar skin microbiota between the two groups. Our study revealed that at the phylum level, patients with VLS had a lower relative abundance of Firmicutes ( < 0.0001) and a higher relative abundance of Proteobacteria than the control group ( < 0.0001). At the genus level, spp. accounted for the largest proportion of the microflora in the asymptomatic controls, while the proportion of spp. in the VLS group was the highest. In the VLS group, the relative abundance of spp., spp., spp., spp., spp., spp. spp., spp., and spp. was significantly increased compared with the control group. Although there was no significant difference in the diversity of the vulvar skin microbiota, the diversity differed significantly between the two groups.
PubMed: 35445011
DOI: 10.3389/fcell.2022.842031 -
Journal of Clinical Medicine Mar 2022Through sperm alteration, semen microbiota tend to be recognized as a cause of infertility, but due to the limited number of studies focusing on this ecological niche,...
Through sperm alteration, semen microbiota tend to be recognized as a cause of infertility, but due to the limited number of studies focusing on this ecological niche, this hypothesis remains controversial. This study aimed to characterize and compare the bacterial communities of sperm samples from patients undergoing couple infertility treatment at the time of diagnosis. The study was prospective (September 2019 to March 2020), monocentric, and focused on alterations of spermatic parameters: count, motility, and morphology. After the amplification of the 16S rDNA (V1 to V3), libraries (n = 91, including 53 patients with abnormalities) were sequenced using the MiSeq platform (Illumina). After quality control processing using a homemade pipeline (QIIME2 modules), the main genera were: Prevotella, Finegoldia, Pseudomonas, Peptinophilus, Streptococcus, Anaerococcus and Corynebacterium. Restricted diversity was observed in samples from patients with abnormal sperm morphology (α-diversity, p < 0.05), whereas diversity increased in patients with an abnormal sperm count (β-diversity, p < 0.05). The enrichment of the genus Prevotella and Haemophilus was observed in negative sperm culture samples and samples with abnormal counts, respectively (p < 0.05). Microbiota differed in their composition according to sperm parameters. Finally, this work highlights the need for the optimization of the management of couples undergoing infertility treatment, possibly by modulating the genital microbiome.
PubMed: 35329834
DOI: 10.3390/jcm11061505 -
PeerJ 2022Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated...
BACKGROUND
Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography.
METHODS
Axillary sweat samples from genetically unrelated individuals ( = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3-V4) of the gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location.
RESULTS
Our study indicated the prevalence of phyla- , , and , consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal-Wallis test, = 0.02), but not with geography ( = 0.62) or diet ( = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R = 0.07, = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of and among individuals of the Pune district. and were abundant in individuals from Ahmednagar whereas, and were abundant in individuals from Nashik district.
CONCLUSION
Our work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals.
Topics: Humans; RNA, Ribosomal, 16S; India; Bacteria; Microbiota; Firmicutes
PubMed: 35313523
DOI: 10.7717/peerj.13075 -
Frontiers in Microbiology 2022Previously, we demonstrated that rectal swabs provide a legitimate alternative to faecal sampling for the assessment of the intestinal microbiota in young piglets....
Previously, we demonstrated that rectal swabs provide a legitimate alternative to faecal sampling for the assessment of the intestinal microbiota in young piglets. However, we also reported that mucosa-adhered microbial populations were more represented in rectal swabs compared to faecal samples, albeit to a degree that varied per swab-sample. Here, we explored the possibility to exploit this variable enrichment of adhered populations in the rectal swabs to assess the impact of diet on mucosa-adhered microbiota in pre-weaning piglets. Paired samples of rectal swabs and colon luminal contents were collected from piglets just before weaning during two independent but similarly designed animal experiments [ = 28 piglets (experiment 1); = 16 piglets (experiment 2)], with an early feeding treatment (EF) group that had access to customised fibrous feed in addition to sow's milk and a control (CON) group exclusively reared on sow's milk. The intestinal microbiome composition in rectal swabs and colon samples collected at 29 days of age were subjected to metataxonomic analysis. The results identified the genera , , and as discriminative taxa enriched in rectal swabs compared to colon. Apart from (10-11% average relative abundance), most of these mucosa-adhered microbial genera display relatively low abundance. Rectal swab microbiota was found to be more variable, which is likely due to variable enrichment of mucosa-adhered microbes. Although almost exclusively driven by one of the experiments, the post-weaning diarrhoea-associated taxa , was enriched in CON compared to the EF group, suggesting that early life feeding may suppress post-weaning-diarrhoea-related problems in piglets. Our findings demonstrate that rectal swabs allow the investigation of the mucosa-adhered microbial populations as a function of dietary treatment in piglets. This offers opportunities to further study dietary approaches that suppress the abundance of the post-weaning diarrhoea associated adherent microbes like . Furthermore, we demonstrate that the paired swab-colon microbiota information (obtained from a subset of animals) can predict the mucosa-adhered populations or "mucosity factor" in rectal swab samples, facilitating the analysis of the adhered microbiota in large animal cohort studies using readily obtainable rectal swabs.
PubMed: 35273582
DOI: 10.3389/fmicb.2022.804986 -
Microbiology Spectrum Feb 2022Cognitive impairment (CI) is among the most common non-motor symptoms of Parkinson's disease (PD), with a substantially negative impact on patient management and...
Cognitive impairment (CI) is among the most common non-motor symptoms of Parkinson's disease (PD), with a substantially negative impact on patient management and outcome. The development and progression of CI exhibits high interindividual variability, which requires better diagnostic and monitoring strategies. PD patients often display sweating disorders resulting from autonomic dysfunction, which has been associated with CI. Because the axillary microbiota is known to change with humidity level and sweat composition, we hypothesized that the axillary microbiota of PD patients shifts in association with CI progression, and thus can be used as a proxy for classification of CI stages in PD. We compared the axillary microbiota compositions of 103 PD patients (55 PD patients with dementia [PDD] and 48 PD patients with mild cognitive impairment [PD-MCI]) and 26 cognitively normal healthy controls (HC). We found that axillary microbiota profiles differentiate HC, PD-MCI, and PDD groups based on differential ranking analysis, and detected an increasing trend in the log ratio of to in progression from HC to PDD. In addition, phylogenetic factorization revealed that the depletion of the , and genera is associated with PD-MCI and PDD. Moreover, functional predictions suggested significant increases in myo-inositol degradation, ergothioneine biosynthesis, propionate biosynthesis, menaquinone biosynthesis, and the proportion of aerobic bacteria and biofilm formation capacity, in parallel to increasing CI. Our results suggest that alterations in axillary microbiota are associated with CI in PD. Thus, axillary microbiota has the potential to be exploited as a noninvasive tool in the development of novel strategies. Parkinson's disease (PD) is the second most common neurodegenerative disease. Cognitive impairment (CI) in PD has significant negative impacts on life quality of patients. The emergence and progression of cognitive impairment shows high variability among PD patients, and thus requires better diagnostic and monitoring strategies. Recent findings indicate a close link between autonomic dysfunction and cognitive impairment. Since thermoregulatory dysfunction and skin changes are among the main manifestations of autonomic dysfunction in PD, we hypothesized that alterations in the axillary microbiota may be useful for tracking cognitive impairment stages in PD. To our knowledge, this the first study characterizing the axillary microbiota of PD patients and exploring its association with cognitive impairment stages in PD. Future studies should include larger cohorts and multicenter studies to validate our results and investigate potential biological mechanisms.
Topics: Aged; Axilla; Bacteria; Cognitive Dysfunction; Female; Humans; Male; Microbiota; Middle Aged; Parkinson Disease; Phylogeny
PubMed: 35138147
DOI: 10.1128/spectrum.02358-21 -
Foot & Ankle Orthopaedics Jul 2021Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or...
BACKGROUND
Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or false-negative growth, leading to ineffective postoperative antibiotic treatment. Next-generation sequencing (NGS) has been explored as an alternative to standard culture in orthopedic infections. NGS is highly sensitive and can detect an entire bacterial genome along with genes conferring antibiotic resistance in a given sample. We investigated the potential use of NGS for accurate identification and quantification of microbes in infected diabetic foot ulcer (DFU). We hypothesize that NGS will aid identification of dominant pathogen and provide a more complete profile of microorganisms in infected DFUs compared to the standard culture method.
METHODS
Data were prospectively collected from 30 infected DFU patients who underwent operative treatment by a fellowship-trained orthopedic foot and ankle surgeon from October 2018 to September 2019. The average age of the patient was 60.4 years. Operative procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-the-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Concordance between the standard culture and NGS was assessed.
RESULTS
In 29 of 30 patients, pathogens were identified by both NGS and culture, with a concordance rate of 70%. In standard culture, (58.6%) was the most common pathogen, followed by coagulase-negative (24.1%), (17.2%), and (17.2%). In NGS, (44.8%) was the most common microorganism followed by (41.4%), and (24.1%). On average, NGS revealed 5.1 (range, 1-11) pathogens in a given sample, whereas culture revealed 2.6 (range, 1-6) pathogens.
CONCLUSION
NGS is an emerging molecular diagnostic method of microbial identification in orthopedic infection. It frequently provides different profiles of microorganisms along with antibiotic-resistant gene information compared to conventional culture in polymicrobial foot infection. Clinical use of NGS for management of foot and ankle infections warrants further investigation.
LEVEL OF EVIDENCE
Level II, diagnostic study.
PubMed: 35097461
DOI: 10.1177/24730114211026933