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Revista Da Associacao Medica Brasileira... 2010The aim of this review is to update knowledge about the vaginal ecosystem, non-cultivation methods for bacterial identification (gene amplification), the Lactobacillus... (Review)
Review
The aim of this review is to update knowledge about the vaginal ecosystem, non-cultivation methods for bacterial identification (gene amplification), the Lactobacillus species that comprise normal vaginal flora and influence of host genetics on bacterial interactions with local innate and acquired immune defenses. A Medline (Pubmed) search from 1997-2009 for relevant articles was performed and the most informative articles were selected. Non-culture techniques (gene amplification) allow a comprehensive analysis of the vaginal ecosystem's composition. In the majority of women in the reproductive age there is a predominance of one or more species of Lactobacillus: L. crispatus, L. inners and L gasseri. However, in other apparently healthy women there is a deficiency or complete absence of Lactobacilli. Instead, there is a substitution by other lactic acid-producing bacteria: Atobium, Megasphaera and/or Leptotrichia species. The infectivity and/or proliferation of pathogenic bacteria in the vagina is suppressed by lactic acid production, by products of endogenous bacteria and by activation of local innate and acquired immunity. Vaginal epithelial cells produce several compounds with anti-microbial activity. These cells have Toll-like receptors on their membrane that recognize molecular patterns associated with pathogens. Recognition leads to production of pro-inflammatory cytokines and stimulation of antigen-specific immunity. The production of IgG and IgA antibodies is also triggered in the endocervix and vagina in response to infection. Vaginal flora composition and the immune mechanisms constitute important defenses. Criteria of normal and abnormal flora have to be reviewed and genetic polymorphism can explain variations in flora composition. This new knowledge should be included in the clinical practice of gynecologists and obstetricians to improve patients care.
Topics: Female; Humans; Lactobacillus; Vagina
PubMed: 20676549
DOI: 10.1590/s0104-42302010000300026 -
Journal of Translational Medicine Aug 2023For many years, the role of the microbiome in tumor progression, particularly the tumor microbiome, was largely overlooked. The connection between the tumor microbiome...
Weighted gene coexpression network analysis and machine learning reveal oncogenome associated microbiome plays an important role in tumor immunity and prognosis in pan-cancer.
BACKGROUND
For many years, the role of the microbiome in tumor progression, particularly the tumor microbiome, was largely overlooked. The connection between the tumor microbiome and the tumor genome still requires further investigation.
METHODS
The TCGA microbiome and genome data were obtained from Haziza et al.'s article and UCSC Xena database, respectively. Separate WGCNA networks were constructed for the tumor microbiome and genomic data after filtering the datasets. Correlation analysis between the microbial and mRNA modules was conducted to identify oncogenome associated microbiome module (OAM) modules, with three microbial modules selected for each tumor type. Reactome analysis was used to enrich biological processes. Machine learning techniques were implemented to explore the tumor type-specific enrichment and prognostic value of OAM, as well as the ability of the tumor microbiome to differentiate TP53 mutations.
RESULTS
We constructed a total of 182 tumor microbiome and 570 mRNA WGCNA modules. Our results show that there is a correlation between tumor microbiome and tumor genome. Gene enrichment analysis results suggest that the genes in the mRNA module with the highest correlation with the tumor microbiome group are mainly enriched in infection, transcriptional regulation by TP53 and antigen presentation. The correlation analysis of OAM with CD8+ T cells or TAM1 cells suggests the existence of many microbiota that may be involved in tumor immune suppression or promotion, such as Williamsia in breast cancer, Biostraticola in stomach cancer, Megasphaera in cervical cancer and Lottiidibacillus in ovarian cancer. In addition, the results show that the microbiome-genome prognostic model has good predictive value for short-term prognosis. The analysis of tumor TP53 mutations shows that tumor microbiota has a certain ability to distinguish TP53 mutations, with an AUROC value of 0.755. The tumor microbiota with high importance scores are Corallococcus, Bacillus and Saezia. Finally, we identified a potential anti-cancer microbiota, Tissierella, which has been shown to be associated with improved prognosis in tumors including breast cancer, lung adenocarcinoma and gastric cancer.
CONCLUSION
There is an association between the tumor microbiome and the tumor genome, and the existence of this association is not accidental and could change the landscape of tumor research.
Topics: Female; Humans; Prognosis; Gene Regulatory Networks; Breast Neoplasms; Ovarian Neoplasms; RNA, Messenger
PubMed: 37573394
DOI: 10.1186/s12967-023-04411-0 -
Microbiology Spectrum Jun 2023Over the past decade, the role of the gut microbiota in many disease states has gained a great deal of attention. Mounting evidence from case-control and observational... (Meta-Analysis)
Meta-Analysis
Over the past decade, the role of the gut microbiota in many disease states has gained a great deal of attention. Mounting evidence from case-control and observational studies has linked changes in the gut microbiota to the pathophysiology of osteoporosis (OP). Nonetheless, the results of these studies contain discrepancies, leaving the literature without a consensus on osteoporosis-associated microbial signatures. Here, we conducted a comprehensive meta-analysis combining and reexamining five publicly available 16S rRNA partial sequence data sets to identify gut bacteria consistently associated with osteoporosis across different cohorts. After adjusting for the batch effect associated with technical variation and heterogeneity of studies, we observed a significant shift in the microbiota composition in the osteoporosis group. An increase in the relative abundance of opportunistic pathogens , , and was observed in the OP group. Moreover, short-chain-fatty-acid (SCFA) producers, including members of the genera , , , , XIV, and , were depleted in the OP group relative to the healthy control (HC) group. Lactic acid-producing bacteria, including , were significantly increased in the OP group. The random forest algorithm further confirmed that these bacteria differentiate the two groups. Furthermore, functional prediction revealed depletion of the SCFA biosynthesis pathway (glycolysis, tricarboxylic acid [TCA] cycle, and Wood-Ljungdahl pathway) and amino acid biosynthesis pathway (methionine, histidine, and arginine) in the OP group relative to the HC group. This study uncovered OP-associated compositional and functional microbial alterations, providing robust insight into OP pathogenesis and aiding the possible development of a therapeutic intervention to manage the disease. Osteoporosis is the most common metabolic bone disease associated with aging. Mounting evidence has linked changes in the gut microbiota to the pathophysiology of osteoporosis. However, which microbes are associated with dysbiosis and their impact on bone density and inflammation remain largely unknown due to inconsistent results in the literature. Here, we present a meta-analysis with a standard workflow, robust statistical approaches, and machine learning algorithms to identify notable microbial compositional changes influencing osteoporosis.
Topics: Humans; Feces; RNA, Ribosomal, 16S; Bacteria; Gastrointestinal Microbiome; Lactobacillales; Osteoporosis
PubMed: 37042756
DOI: 10.1128/spectrum.00322-23 -
Animal Nutrition (Zhongguo Xu Mu Shou... Jun 2022Shaziling pig, a Chinese indigenous breed, has been classified as a fatty pig model. However, the gut microbial development and role in lipid metabolism in Shaziling...
Shaziling pig, a Chinese indigenous breed, has been classified as a fatty pig model. However, the gut microbial development and role in lipid metabolism in Shaziling pigs has been rarely reported. Here, we compared the lipid metabolic and microbial profiles at 30, 60, 90, 150, 210, and 300 d of age between Shaziling and Yorkshire pigs. Predictably, there were marked differences in the liver lipids (i.e., cholesterol, glucose, and low-density lipoprotein) and the lipid related expressions (i.e., , /, /, and -) between Shaziling and Yorkshire pigs. Bacteria sequencing in the ileal digesta and mucosa showed that Shaziling pigs had a higher α-diversity and higher abundances of probiotics, such as , , and . Thirty-five differentiated metabolites were further identified in the mucosa between Shaziling and Yorkshire pigs, which were enriched in the carbohydrate, protein, glucose and amino acid metabolism and bile acid biosynthesis. Furthermore, 7 differentiated microbial species were markedly correlated with metabolites, indicating the role of gut microbiota in the host metabolism. Next, the role of differentiated in lipid metabolism was validated in Duroc × Landrace × Yorkshire (DLY) pigs and the results showed that mono-colonization promoted lipid deposition and metabolism by altering gut microbiota (i.e., and ) and // gene expressions. In conclusion, Shaziling pigs exhibited different metabolic and microbial profiles compared with Yorkshire pigs, which might have contributed to the diverse metabolic phenotypes, and the significant enrichment of in Shaziling pigs promoted lipid metabolism and obesity of DLY pigs, which provided a novel idea to improve the fat content of lean pigs.
PubMed: 35600540
DOI: 10.1016/j.aninu.2021.10.012 -
Foods (Basel, Switzerland) Nov 2022The appropriate domestic cooking methods can retain and protect the biological properties of foods well. Thus, the objective of this study was to unravel the effect of...
The appropriate domestic cooking methods can retain and protect the biological properties of foods well. Thus, the objective of this study was to unravel the effect of different cooking methods on the microbiota modulatory properties of yam and their non-starch polysaccharides by an in vitro simulated digestion and fermentation model. The results showed that different cooking processes led to different changes in polysaccharide content. The polysaccharide content of yam increased by 21.3~108.2% or decreased by 12.0% compared with that of raw yam. Additionally, the soluble polysaccharides contents in all cooked yam samples significantly increased by 16.85~119.97% after in vitro digestion. The regulation of whole-yam digesta on gut microbiota was partly related with yam polysaccharides. Both yam and yam polysaccharide fermentation appeared to promote beneficial bacteria, such as , spp. and and suppressed bacterial pathogens such as and . Household cooking significantly influenced the prebiotic performances of yam and yam polysaccharides by changing the heat-sensitive microbial substrates and their physiology properties. According to our results, normal-pressure steaming and normal-pressure boiling processes can retain the microbiota modulatory effects of Chinese yam.
PubMed: 36496601
DOI: 10.3390/foods11233794 -
Frontiers in Microbiology 2022A red yeast isolated from orange and grape soil and identified by the 26S rDNA sequence analysis revealed that it was and named TZR. Its biomass and carotenoid...
A red yeast isolated from orange and grape soil and identified by the 26S rDNA sequence analysis revealed that it was and named TZR. Its biomass and carotenoid production reached a maximum when using the fermentation medium with pH 6.0, containing 5% glucose, 1% peptone, and 1.5% yeast powder. TZR was resistant to 55°C for 15 min, 0.2% pig bile salts for 4 h, and artificial gastric and intestinal fluids. A total of thirty 28-day weaned pigs were divided into three groups, and the piglets were fed a basal diet (CON), a basal diet and orally administered 1 ml 1.0 × 10 CFU/ml DSM 2361 three times (), or a basal diet and orally administered 1 ml 1.0 × 10 CFU/mL TZR three times daily () for 4 weeks. Compared with the piglets in the CON group, those in the or group reported an increased average daily weight gain and average daily feed intake ( < 0.05) and a decreased feed/gain ( < 0.05). The diarrhea rate of piglets in the group was lower than that in the CON and groups ( < 0.05). Compared with that in the CON and groups, the group reported an increased ileum villus height ( < 0.05), serum concentration of total antioxidant content, total superoxide dismutase, and glutathione peroxidase and pepsin and lipase activities in the intestinal content, while it reported a decreased serum concentration of malondialdehyde and pH of the intestinal tract ( < 0.05). The relative abundances of and of caecum in the group were lower than those in the CON and group ( < 0.05). The relative abundances of , and of caecum in the group were higher than those in the CON and group ( < 0.05). TZR can produce carotenoids and adapts to the animal's gastrointestinal environment. Oral TZR improved growth performance, enhanced antioxidant capacity, strengthened gastrointestinal digestion, and maintained the intestinal microbiological balance of piglets.
PubMed: 35903473
DOI: 10.3389/fmicb.2022.922136 -
Microbial Genomics Dec 2021The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual...
The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well characterized. Here, we examine two vaginal bacterial taxa grouped within the genus that have been previously associated with bacterial vaginosis (BV) and pregnancy complications. Phylogenetic analyses support the classification of these taxa as two distinct species. These two phylotypes, phylotype 1 (MP1) and phylotype 2 (MP2), differ in genomic structure and metabolic potential, suggestive of differential roles within the vaginal environment. Further, these vaginal taxa show evidence of genome reduction and changes in DNA base composition, which may be common features of host dependence and/or adaptation to the vaginal environment. In a cohort of 3870 women, we observed that MP1 has a stronger positive association with bacterial vaginosis whereas MP2 was positively associated with trichomoniasis. MP1, in contrast to MP2 and other common BV-associated organisms, was not significantly excluded in pregnancy. In a cohort of 52 pregnant women, MP1 was both present and transcriptionally active in 75.4 % of vaginal samples. Conversely, MP2 was largely absent in the pregnant cohort. This study provides insight into the evolutionary history, genomic potential and predicted functional role of two clinically relevant vaginal microbial taxa.
Topics: Bacterial Proteins; Base Composition; Case-Control Studies; Evolution, Molecular; Female; Gene Expression Regulation, Bacterial; Genome Size; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Humans; Megasphaera; Phylogeny; Pregnancy; RNA, Ribosomal, 16S; Reproductive Health; Sequence Analysis, DNA; Vagina; Vaginosis, Bacterial
PubMed: 34898422
DOI: 10.1099/mgen.0.000526 -
Disease Markers 2022The study analyzed gut microflora's composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric...
BACKGROUND
The study analyzed gut microflora's composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric patients with acute appendicitis.
METHODS
High-throughput sequencing and bioinformatics analysis were used to investigate the composition and diversity of gut microflora in 20 pediatric patients with acute appendicitis and 11 healthy children. Endpoints measured were operational taxonomic units (OTU) of gut microflora. The OTU and its abundance analysis, sample diversity analysis, principal component analysis of samples, differential analysis, and analysis of biomarkers were performed.
RESULTS
Overall fecal microbial richness and diversity were similar in patients and controls. Yet richness within the group of Bilophila, Eggerthella, Clostridium, Parvimonas, Megasphaera, Atopobium, Phascolarctobacterium, Adlercreutzia, Barnesiella, Klebsiella, Enterococcus, and Prevotella genera was higher in patients. Adlercreutzia was significantly positively correlated with IL-10, while the three other genera, comprising Klebsiella, Adlercreutzia, and Prevotella, were positively correlated with B cells level.
CONCLUSION
Gut microbiome components are significantly different in pediatric patients with acute appendicitis and healthy children. The differential abundance of some genera is correlated with the production of inflammatory markers in appendicitis.
Topics: Appendicitis; Biomarkers; Child; Dysbiosis; Feces; Gastrointestinal Microbiome; Humans
PubMed: 35845131
DOI: 10.1155/2022/1059445 -
Microorganisms Jan 2022Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown...
Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, 7, , , , , and in the rumen of the EW group had greater relative abundances. At 35 d, the _NK3A20_group was enriched in CON. On 63 d, _UCG-002 was abundant in EW. and in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of _UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of , , and _UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.
PubMed: 35056593
DOI: 10.3390/microorganisms10010144 -
Microorganisms Jan 2024The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use... (Review)
Review
The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of to produce C-C carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
PubMed: 38276203
DOI: 10.3390/microorganisms12010219