scholarly journals The Obesity-Related Gut Bacterial and Viral Dysbiosis Can Impact the Risk of Colon Cancer Development

2020 ◽  
Vol 8 (3) ◽  
pp. 431 ◽  
Author(s):  
Giuseppina Campisciano ◽  
Nicolò de Manzini ◽  
Serena Delbue ◽  
Carolina Cason ◽  
Davide Cosola ◽  
...  
Keyword(s):  
Cell Transformation ◽  
Bacterial Species ◽  
Oncogenic Viruses ◽  
Tumor Patients ◽  
Microbiome Composition ◽  
Microbial Profile ◽  
Bk Polyomavirus ◽  
Obese Subjects ◽  
Colon Rectal Cancer ◽  
Obesity And Cancer

An incorrect food regimen from childhood is suggested to negatively impact the gut microbiome composition leading to obesity and perhaps to colon rectal cancer (CRC) in adults. In this study, we show that the obesity and cancer gut microbiota share a characteristic microbial profile with a high colonization by mucin degraders species, such as Hafnia alvei and Akkermansia muciniphila. In addition, the species Clostridium bolteae, a bacterium associated with insulin resistance, dyslipidemia, and inflammation, has been associated with the presence of oncogenic Human Polyomaviruses (HPyVs). Merkel cell Polyomavirus (MCPyV) and BK Polyomavirus (BKPyV) were the most frequently oncogenic viruses recovered in the gut of both obese and tumor patients. Considering the high seroprevalence of HPyVs in childhood, their association with specific bacterial species deserve to be further investigated. Data from the present study highlight the presence of a similar microbiome pattern in CRC and obese subjects, suggesting that obese microbiome may represent an opportunity for tumorigenic/driver bacteria and viruses to trigger cell transformation.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis

Nutrients ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1395 ◽  
Author(s):  
Shehnaz K. Hussain ◽  
Tien S. Dong ◽  
Vatche Agopian ◽  
Joseph R. Pisegna ◽  
Francisco A. Durazo ◽  
...  
Keyword(s):  
Liver Cirrhosis ◽  
Diet Quality ◽  
Alpha Diversity ◽  
Healthy Eating Index ◽  
Sequencing Data ◽  
Microbiome Composition ◽  
Coffee Drinking ◽  
Microbial Profile ◽  
Protein Fiber ◽  
Fiber Consumption

The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness (p = 0.03) and a different microbial profile compared to those with lower adherence (p = 0.03). Prevotella-9 and Agathobacter were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile (p = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness (p = 0.001), and there was a dose–response association between coffee drinking and relative abundance of Veillonella (p = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.

scholarly journals Gut Microbiome: Profound Implications for Diet and Disease

Nutrients ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 1613 ◽  
Author(s):  
Ronald Hills ◽  
Benjamin Pontefract ◽  
Hillary Mishcon ◽  
Cody Black ◽  
Steven Sutton ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Short Chain Fatty Acids ◽  
E Coli ◽  
Beneficial Effects ◽  
Microbial Profile ◽  
Irritable Bowel ◽  
Prebiotic Fiber

The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual’s starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions including obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease.

Alterations in the uterine microbiome in patients with early endometrial cancer: Variations by ethnicity and obesity.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e17114-e17114
Author(s):  
Leslie Horn Clark ◽  
Temitope O Keku ◽  
Nicole Amber McCoy ◽  
Gabrielle Hawkins ◽  
Victoria Lin Bae-Jump ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Clinical Outcomes ◽  
High Throughput Sequencing ◽  
Tumor Grade ◽  
Microbiota Composition ◽  
Obesity Status ◽  
Obese Subjects ◽  
Grade 3 ◽  
Obesity And Cancer ◽  
Relationship Of

e17114 Background: Obesity and race are known to negatively impact clinical outcomes in endometrial cancer (EC). Mounting evidence suggests the gut microbiome may play an important role in the pathogenesis of both obesity and cancer, however, little is known about the microbiome of the malignant uterus. Further, there is known to be microbiome variability by ethnicity in the vagina and gut. Thus, we sought to evaluate the microbiota of ECs and to assess for variations by obesity and race. Methods: Following IRB approval, banked tumor specimens of patients undergoing hysterectomy for management of endometrioid EC were identified. Tumors were analyzed from African-American (AA) and Caucasian (CAU) patients and stratified as obese (BMI ≥ 30kg/m2) or non-obese (BMI < 30kg/m2). The microbiota of the endometrial tumors were characterized by 16S rRNA high throughput sequencing. Descriptive statistics were performed. Results: We evaluated specimens from 11 AA (52%) and 10 CAU (48%). The median age was 68.9 years. Majority of women were postmenopausal (n=17, 81%) and obese (n=14, 66.7%). Tumor grade was evenly distributed with 7 grade 1 (33.3%), 6 grade 2 (28.6%), and 8 grade 3 tumors (38.1%). We found that EC microbiota richness was higher in AA than CAU (p=0.02). When analyzed by race and obesity status, we observed significant differences in EC microbiota composition. The microbiota composition differed between obese AA and obese CAU (p=0.04). In obese subjects the distribution of Proteobacteria was 55% AA vs. 30.7% CAU (p=0.02) while Actinobacteria abundance was 17.8% versus 34.4% (p=0.05) (Table 1). Among CAU, the EC microbiota profile differed between obese and non-obese (p=0.07). At the genus level, the relative abundances of Delftia, Finelgoldia, Geobacillus, Propionibacterium and Pseudomonasvaried by obesity and race. Conclusions: Bacteria exist in the malignant uterus. EC microbiota diversity was greater in tumors of AA versus CAU women, and tumor microbiota profiles were distinct between ECs of obese and lean women. Better understanding of the inter-relationship of obesity and race on the EC microbiota may provide critical insight into the disparate clinical outcomes between AA and CAU women with EC.

scholarly journals Anion homeostasis is important for non-lytic release of BK polyomavirus from infected cells

Open Biology ◽  
2015 ◽  
Vol 5 (8) ◽  
pp. 150041 ◽  
Author(s):  
Gareth L. Evans ◽  
Laura G. Caller ◽  
Victoria Foster ◽  
Colin M. Crump
Keyword(s):  
Anion Channel ◽  
Oncogenic Viruses ◽  
Viral Capsids ◽  
Transplant Patients ◽  
Bk Polyomavirus ◽  
Infected Cells ◽  
Homeostasis Regulation ◽  
Acidic Organelles ◽  
Dose Dependent ◽  
Dose Dependent Effect

BK polyomavirus (BKPyV) is a member of a family of potentially oncogenic viruses, whose reactivation can cause severe pathological conditions in transplant patients, leading to graft rejection. As with many non-enveloped viruses, it is assumed that virus release occurs through lysis of the host cell. We now show the first evidence for a non-lytic release pathway for BKPyV and that this pathway can be blocked by the anion channel inhibitor DIDS. Our data show a dose-dependent effect of DIDS on the release of BKPyV virions. We also observed an accumulation of viral capsids in large LAMP-1-positive acidic organelles within the cytoplasm of cells upon DIDS treatment, suggesting potential late endosome or lysosome-related compartments are involved in non-lytic BKPyV release. These data highlight a novel mechanism by which polyomaviruses can be released from infected cells in an active and non-lytic manner, and that anion homeostasis regulation is important in this pathway.

scholarly journals Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Olga M. Pérez-Carrascal ◽  
Nicolas Tromas ◽  
Yves Terrat ◽  
Elisa Moreno ◽  
Alessandra Giani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heterotrophic Bacteria ◽  
Bacterial Species ◽  
Colony Growth ◽  
Genomic Diversity ◽  
Gene Copy ◽  
Metagenomic Sequencing ◽  
Associated Bacteria ◽  
Microbiome Composition

Abstract Background Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies—including cyanobacteria and associated bacterial genomes—isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. Results We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting. Conclusions We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations.

scholarly journals The Vaginal Microbiome: A Long Urogenital Colonization Throughout Woman Life

2021 ◽  
Vol 11 ◽  
Author(s):  
Renata S. Auriemma ◽  
Roberta Scairati ◽  
Guendalina del Vecchio ◽  
Alessia Liccardi ◽  
Nunzia Verde ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Hormone Replacement Therapy ◽  
Bacterial Species ◽  
Hormone Replacement ◽  
Vaginal Microbiome ◽  
Microbiome Composition ◽  
Post Menopausal ◽  
Lines Of Evidence

Vaginal microbial niche is a dynamic ecosystem, composed by more than 200 bacterial species which are influenced by genes, ethnic background and environmental-behavioral factors. Several lines of evidence have well documented that vaginal microbiome constantly changes over the course of woman’s life, so to exert an important impact on woman quality of life, from newborn to post-menopausal ages. This review aims at analyzing the role of vaginal microbiome in the maintenance of woman’s homeostasis and at tracking critical changes that commonly occur across woman’s lifetime. The role of hormone replacement therapy in the modulation of vaginal microbiome composition and in the improvement of vaginal wellness in postmenopausal women with decreasing levels of circulating estrogen is discussed.

scholarly journals Positive Synergistic Effects of Quercetin and Rice Bran on Human Gut Microbiota Reduces Enterobacteriaceae Family Abundance and Elevates Propionate in a Bioreactor Model

2021 ◽  
Vol 12 ◽  
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Ranjini Sankaranarayanan ◽  
Elizabeth P. Ryan ◽  
G. Jayarama Bhat ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Rice Bran ◽  
Synergistic Effects ◽  
Bacterial Species ◽  
Positive Influence ◽  
Human Gut ◽  
Fatty Acid Production ◽  
Microbiome Composition ◽  
Human Gut Microbiota

Dietary fiber and flavonoids have substantial influence on the human gut microbiota composition that significantly impact health. Recent studies with dietary supplements such as quercetin and rice bran have shown beneficial impacts on the host alongside a positive influence of the gut microbiota. The specific bacterial species impacted by quercetin or rice bran in the diet is not well understood. In this study, we used a minibioreactor array system as a model to determine the effect of quercetin and rice bran individually, as well as in combination, on gut microbiota without the confounding host factors. We found that rice bran exerts higher shift in gut microbiome composition when compared to quercetin. At the species level, Acidaminococcus intestini was the only significantly enriched taxa when quercetin was supplemented, while 15 species were enriched in rice bran supplementation and 13 were enriched when quercetin and rice bran were supplemented in combination. When comparing the short chain fatty acid production, quercetin supplementation increased isobutyrate production while propionate dominated the quercetin and rice bran combined group. Higher levels of propionate were highly correlated to the lower abundance of the potentially pathogenic Enterobacteriaceae family. These findings suggest that the combination of quercetin and rice bran serve to enrich beneficial bacteria and reduce potential opportunistic pathogens. In vivo studies are necessary to determine how this synergy of quercetin and rice bran on microbiota impact host health.

scholarly journals Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microsporidian Infection ◽  
Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

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