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Nutrients Dec 2021Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using... (Meta-Analysis)
Meta-Analysis
Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (-0.06, 95% CI -0.24, 0.12, = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, = 86%). At the genus level, lower relative proportions of and and higher , , , , , , , , , , , , and were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.
Topics: Bacteria; Feces; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; Obesity
PubMed: 35010887
DOI: 10.3390/nu14010012 -
European Urology Jun 2021Little is known about the role of the genitourinary and gastrointestinal microbiota in the pathogenesis of male infertility.
BACKGROUND
Little is known about the role of the genitourinary and gastrointestinal microbiota in the pathogenesis of male infertility.
OBJECTIVE
To compare the taxonomic and functional profiles of the gut, semen, and urine microbiomes of infertile and fertile men.
DESIGN, SETTING, AND PARTICIPANTS
We prospectively enrolled 25 men with primary idiopathic infertility and 12 healthy men with proven paternity, and we collected rectal swabs, semen samples, midstream urine specimens, and experimental controls.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS
We performed comprehensive semen analysis, 16S rRNA sequencing for quantitative high-resolution taxonomy, and shotgun metagenomics with a median of 140 million reads per sample for functional metabolic pathway profiling.
RESULTS AND LIMITATIONS
We identified a diverse semen microbiome with modest similarity to the urinary microbiome. Infertile men harbored increased seminal α-diversity and distinct β-diversity, increased seminal Aerococcus, and decreased rectal Anaerococcus. Prevotella abundance was inversely associated with sperm concentration, and Pseudomonas was directly associated with total motile sperm count. Vasectomy appeared to alter the seminal microbiome, suggesting a testicular or epididymal contribution. Anaerobes were highly over-represented in the semen of infertile men with a varicocele, but oxidative stress and leukocytospermia were associated with only subtle differences. Metagenomics data identified significant alterations in the S-adenosyl-L-methionine cycle, which may play a multifaceted role in the pathogenesis of infertility via DNA methylation, oxidative stress, and/or polyamine synthesis.
CONCLUSIONS
This pilot study represents the first comprehensive investigation into the microbiome in male infertility. These findings provide the foundation for future investigations to explore causality and identify novel microbiome-based diagnostics and therapeutics for men with this complex and emotionally devastating disease.
PATIENT SUMMARY
We explored the resident populations of bacteria living in the gut, semen, and urine of infertile and fertile men. We found several important bacterial and metabolic pathway differences with the potential to aid in diagnosing and treating male infertility in the future.
Topics: Dysbiosis; Humans; Infertility, Male; Male; Microbiota; Pilot Projects; RNA, Ribosomal, 16S; Semen; Sperm Motility
PubMed: 33573862
DOI: 10.1016/j.eururo.2021.01.014 -
BMC Infectious Diseases Aug 2020In this study, the association between human papillomavirus (HPV) infection and related cervical intraepithelial neoplasia (CIN) or cervical cancer and vaginal...
BACKGROUND
In this study, the association between human papillomavirus (HPV) infection and related cervical intraepithelial neoplasia (CIN) or cervical cancer and vaginal microbiome was evaluated in Chinese cohorts.
METHODS
The vaginal bacterial composition of five groups, HPV-infected women without CINs (HPV, n = 78), women with low-grade squamous intraepithelial lesions (LSIL, n = 51), women with high-grade squamous intraepithelial lesions (HSIL, n = 23), women with invasive cervical cancer (Cancer, n = 9) and healthy women without HPV infection (Normal, n = 68), was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V3-4) using Illumina MiSeq.
RESULTS
HPV infection increased vaginal bacterial richness and diversity regardless of the status of CINs. The vaginal bacterial richness and diversity were further augmented in women with cervical cancer. Lactobacillus was the most abundant genus in all groups. HPV infection had a negative influence on the abundances of Lactobacillus, Gardnerella and Atopobium. Accordingly, HPV infection increased the relative abundance of Prevotella, Bacillus, Anaerococcus, Sneathia, Megasphaera, Streptococcus and Anaerococcus. The increased proportions of Bacillus, Anaerococcus and the reduced abundance of Gradnerella vaginalis were probably related with the progression of CINs severity. HPV infection without CINs or cancerous lesions was strongly associated with Megasphaera. The most abundant bacterium in the LSIL group was Prevotella amnii. However, Prevotella timonensis, Shuttleworthia and Streptococcaceae at the family level were three taxa related to HSIL. Furthermore, more taxa were associated with the Cancer group including Bacillus, Sneathia, Acidovorax, Oceanobacillus profundus, Fusobacterium, Veillonellaceae at the family level, Anaerococcus and Porphyromonas uenonis. Samples in the Normal group were mostly assigned to CST III. HPV infection converted the vaginal bacterial community structure from CST III to CST IV. Furthermore, the proportions of CST IV were gradually augmented with the progression of the severity of CINs.
CONCLUSIONS
This work interpreted the differential vaginal bacteria under HPV infection and various precancerous or cancerous lesions in a Chinese cohort. We distinguished the specific microbes and the vaginal bacterial structure that were related with the progression of CINs severity in Chinese women.
Topics: Adult; Aged; Biodiversity; China; Cohort Studies; Disease Progression; Female; Humans; Lactobacillus; Microbiota; Middle Aged; Papillomaviridae; Papillomavirus Infections; RNA, Ribosomal, 16S; Uterine Cervical Neoplasms; Vagina; Uterine Cervical Dysplasia
PubMed: 32842982
DOI: 10.1186/s12879-020-05324-9 -
Genome Medicine Apr 2021Currently, over half of breast cancer cases are unrelated to known risk factors, highlighting the importance of discovering other cancer-promoting factors. Since...
BACKGROUND
Currently, over half of breast cancer cases are unrelated to known risk factors, highlighting the importance of discovering other cancer-promoting factors. Since crosstalk between gut microbes and host immunity contributes to many diseases, we hypothesized that similar interactions could occur between the recently described breast microbiome and local immune responses to influence breast cancer pathogenesis.
METHODS
Using 16S rRNA gene sequencing, we characterized the microbiome of human breast tissue in a total of 221 patients with breast cancer, 18 individuals predisposed to breast cancer, and 69 controls. We performed bioinformatic analyses using a DADA2-based pipeline and applied linear models with White's t or Kruskal-Wallis H-tests with Benjamini-Hochberg multiple testing correction to identify taxonomic groups associated with prognostic clinicopathologic features. We then used network analysis based on Spearman coefficients to correlate specific bacterial taxa with immunological data from NanoString gene expression and 65-plex cytokine assays.
RESULTS
Multiple bacterial genera exhibited significant differences in relative abundance when stratifying by breast tissue type (tumor, tumor adjacent normal, high-risk, healthy control), cancer stage, grade, histologic subtype, receptor status, lymphovascular invasion, or node-positive status, even after adjusting for confounding variables. Microbiome-immune networks within the breast tended to be bacteria-centric, with sparse structure in tumors and more interconnected structure in benign tissues. Notably, Anaerococcus, Caulobacter, and Streptococcus, which were major bacterial hubs in benign tissue networks, were absent from cancer-associated tissue networks. In addition, Propionibacterium and Staphylococcus, which were depleted in tumors, showed negative associations with oncogenic immune features; Streptococcus and Propionibacterium also correlated positively with T-cell activation-related genes.
CONCLUSIONS
This study, the largest to date comparing healthy versus cancer-associated breast microbiomes using fresh-frozen surgical specimens and immune correlates, provides insight into microbial profiles that correspond with prognostic clinicopathologic features in breast cancer. It additionally presents evidence for local microbial-immune interplay in breast cancer that merits further investigation and has preventative, diagnostic, and therapeutic potential.
Topics: Aged; Anti-Bacterial Agents; Breast; Breast Neoplasms; Case-Control Studies; Female; Humans; Microbiota; Middle Aged; Phylogeny; Prognosis; Risk Factors
PubMed: 33863341
DOI: 10.1186/s13073-021-00874-2 -
Scientific Reports Sep 2021Bacterial species and their role in delaying the healing of pressure ulcers (PU) in spinal cord injury (SCI) patients have not been well described. This pilot study...
Bacterial species and their role in delaying the healing of pressure ulcers (PU) in spinal cord injury (SCI) patients have not been well described. This pilot study aimed to characterise the evolution of the cutaneous microbiota of PU in SCI cohort. Twenty-four patients with SCI from a French neurological rehabilitation centre were prospectively included. PU tissue biopsies were performed at baseline (D0) and 28 days (D28) and analysed using 16S rRNA gene-based sequencing analysis of the V3-V4 region. At D0, if the overall relative abundance of genus highlighted a large proportion of Staphylococcus, Anaerococcus and Finegoldia had a significantly higher relative abundance in wounds that stagnated or worsened in comparison with those improved at D28 (3.74% vs 0.05%; p = 0.015 and 11.02% versus 0.16%; p = 0.023, respectively). At D28, Proteus and Morganella genera were only present in stagnated or worsened wounds with respectively 0.02% (p = 0.003) and 0.01% (p = 0.02). Moreover, Proteus, Morganella, Anaerococcus and Peptoniphilus were associated within the same cluster, co-isolated from biopsies that had a poor evolution. This pathogroup could be a marker of wound degradation and Proteus could represent a promising target in PU management.
Topics: Aged; Bacteria; Female; Humans; Male; Microbiota; Middle Aged; Pressure Ulcer; RNA, Ribosomal, 16S; Wound Healing
PubMed: 34531517
DOI: 10.1038/s41598-021-98073-x -
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 -
Archives of Microbiology Jul 2022Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics...
Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics approach. The 16S rRNA gene sequences of each strain were sequenced and then compared by BLASTn to the NCBI database. Strains Marseille-Q5893 and Marseille-Q5883 were most closely related to Anaerococcus obesiensis and Finegoldia magna, with identities of 98.5% and 90.0%, respectively. Strain Marseille-Q5893 is strictly anaerobic, while strain Marseille-Q5883 is facultative anaerobic. Both strains are Gram-positive, coccus-shaped, oxidase- and catalase-negative. The most abundant fatty acid for both strains is hexadecanoic acid, followed by 9-octadecenoic acid and tetradecanoic acid. Strain Marseille-Q5893 has a genome size of 1,831,271 bp with a G+C content of 29.4 mol%, whereas strain Marseille-Q5883 has a genome of 1,997,945 bp with a 33.6 mol% G+C content. The genomic comparison of closely related species with strains Marseille-Q5893 and Marseille-Q5883 showed that all digital DNA-DNA hybridization (dDDH) and orthologous average nucleotide identity (OrthoANI) values were lower than the published species thresholds (70% and 95-96%, respectively). Based on these data, we conclude that strain Marseille-Q5893 belongs to a new species in the family Peptoniphilaceae and strain Marseille-Q5883 belongs to a new genus in the family Peptostreptococcaceae. For these two new bacterial species, the names Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., were proposed.
Topics: Base Composition; Clostridiales; DNA, Bacterial; Fatty Acids; Female; Humans; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35859139
DOI: 10.1007/s00203-022-03082-7 -
Journal of Medical Microbiology Mar 2024There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including spp., spp., spp., spp.,... (Review)
Review
There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including spp., spp., spp., spp., spp., spp spp and spp. linked to multiple cancer types. In this review we explore these pathogenic associations. The mechanisms by which bacteria are known or predicted to interact with human cells are reviewed and we present an overview of the interlinked mechanisms and hypotheses of how multiple intracellular anaerobic bacterial pathogens may act together to cause host cell and tissue microenvironment changes associated with carcinogenesis and cancer cell invasion. These include combined effects on changes in cell signalling, DNA damage, cellular metabolism and immune evasion. Strategies for early detection and eradication of anaerobic cancer-associated bacterial pathogens that may prevent cancer progression are proposed.
Topics: Humans; Bacteria, Anaerobic; Carcinogenesis; Immune Evasion; Porphyromonas; Signal Transduction; Tumor Microenvironment
PubMed: 38535967
DOI: 10.1099/jmm.0.001817 -
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 -
Current Sexual Health Reports Sep 2020Focusing on studies published within the last decade, we review the literature on the seminal microbiome and male factor infertility. We highlight potential mechanisms...
PURPOSE OF REVIEW
Focusing on studies published within the last decade, we review the literature on the seminal microbiome and male factor infertility. We highlight potential mechanisms by which microbes may impact fertility and underscore key limitations and clinical implications of these studies.
RECENT FINDINGS
The seminal microbiome encompasses a metabolically and phylogenetically diverse group of microorganisms. was consistently associated with normal semen analysis parameters and fertility; was negatively associated with semen quality. These microbes may participate in a complex cross-talk with the host immune system, thereby modulating local and perhaps systemic inflammatory responses, impacting semen quality.
SUMMARY
Research investigating the intersection between the seminal microbiome and male fertility is still in its infancy. Recent investigations have been exclusively cross-sectional, correlational studies, limiting the clinical applicability of published research. Prospective studies with more sophisticated methodologies are necessary.
PubMed: 33746642
DOI: 10.1007/s11930-020-00273-5