Microbiome analysis reveals the significant changes in gut microbiota of diarrheic Baer's Pochards (Aythya baeri)

AbstractPurposeThe lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated to the abysmal survival rate in patients. In addition to several potential detection tools under active investigation, we tested the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high-risk for PDAC.Experimental DesignA combination of 16s pyrosequencing and whole-genome sequencing of gut microbiota was used in a spontaneous genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC). Metabolic reconstruction of microbiome was done using the HUmanN2 pipeline. Serum polyamine levels were measured from murine and patient samples using standard methods.ResultsResults showed a progressive Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentration. Therefore, at the early stages of tumorigenesis, the gut microbial composition changes in a way to release metabolites that foster host tumorigenesis, thereby fulfilling the ‘vicious cycle hypothesis’ of the role of the microbiome in health and disease states.ConclusionsOur results provide a potential, precise, non-invasive tool for early detection of PDAC, which will result in improved outcomes.SynopsisGut microbiota changes during early stages of pancreatic ductal adenocarcinoma (PDAC) progression and contributes towards host polyamine pool. Both changes can be used as an early predictive marker for PDAC.Translational RelevancePancreatic carcinogenesis progresses through pre-cancerous PanIN lesions to invasive cancer. Even though these morphological changes are histologically distinct, imaging techniques are not able to distinguish the pre-invasive PanINs from normal pancreas, making detection of a tumor at a precancerous stage impossible. Thus, majority of cases (85–90%) present with advanced pancreatic cancer at the time of diagnosis. This contributes to the dismal survival rate in this disease. Our study of gut microbiome analysis on KPC mice during tumor progression followed by metabolic reconstruction and experimental validation in human samples indicate that gut-microbiome analysis along with an analysis of the microbial metabolites can be developed as potential biomarkers for detection of PDAC at early stages when histological changes are not yet grossly apparent.

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Microbiome analysis reveals the alterations in gut microbiota in different intestinal segments of Yimeng black goats

Microbial Pathogenesis ◽

10.1016/j.micpath.2021.104900 ◽

2021 ◽

pp. 104900

Author(s):

Aoyun Li ◽

Yan Yang ◽

Yan Zhang ◽

Shenjin Lv ◽

Taihua Jin ◽

...

Keyword(s):

Gut Microbiota ◽

Microbiome Analysis ◽

Intestinal Segments

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Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites

Cells ◽

10.3390/cells10113243 ◽

2021 ◽

Vol 10 (11) ◽

pp. 3243

Author(s):

Orazio Palmieri ◽

Stefano Castellana ◽

Giuseppe Biscaglia ◽

Anna Panza ◽

Anna Latiano ◽

...

Keyword(s):

Ulcerative Colitis ◽

Gut Microbiota ◽

Ileoanal Pouch ◽

Bacterial Strains ◽

Microbial Composition ◽

Novel Treatments ◽

Microbiome Analysis ◽

Unknown Species ◽

Healthy Control

The pathogenesis of ulcerative colitis (UC) is unknown, although genetic loci and altered gut microbiota have been implicated. Up to a third of patients with moderate to severe UC require proctocolectomy with ileal pouch ano-anastomosis (IPAA). We aimed to explore the mucosal microbiota of UC patients who underwent IPAA. Methods: For microbiome analysis, mucosal specimens were collected from 34 IPAA individuals. Endoscopic and histological examinations of IPAA were normal in 21 cases, while pouchitis was in 13 patients. 19 specimens from the healthy control (10 from colonic and 9 from ileum) were also analyzed. Data were analyzed using an ensemble of software packages: QIIME2, coda-lasso, clr-lasso, PICRUSt2, and ALDEx2. Results: IPAA specimens had significantly lower bacterial diversity as compared to normal. The microbial composition of the normal pouch was also decreased also when compared to pouchitis. Faecalibacterium prausnitzii, Gemmiger formicilis, Blautia obeum, Ruminococcus torques, Dorea formicigenerans, and an unknown species from Roseburia were the most uncommon in pouch/pouchitis, while an unknown species from Enterobacteriaceae was over-represented. Propionibacterium acnes and Enterobacteriaceae were the species most abundant in the pouchitis and in the normal pouch, respectively. Predicted metabolic pathways among the IPAA bacterial communities revealed an important role of immunometabolites such as SCFA, butyrate, and amino acids. Conclusions: Our findings showed specific bacterial signature hallmarks of dysbiosis and could represent bacterial biomarkers in IPAA patients useful to develop novel treatments in the future by modulating the gut microbiota through the administration of probiotic immunometabolites-producing bacterial strains and the addition of specific prebiotics and the faecal microbiota transplantation.

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Fecal Fermentation Profile, Serum Fatty Acid Profile and Measures of Liver Health in Male HIV-infected Versus Non-infected Controls

Current Developments in Nutrition ◽

10.1093/cdn/nzaa040_004 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 4-4

Author(s):

Mary Andreae ◽

W Andrew Clark ◽

John Sterrett ◽

James Adkins ◽

Konner Smith ◽

...

Keyword(s):

Fatty Acid ◽

Liver Fibrosis ◽

Gut Microbiota ◽

Liver Damage ◽

Volatile Fatty Acids ◽

Statistical Significance ◽

Blood Draw ◽

Microbiome Analysis ◽

Freeze Dried ◽

Fermentation Profile

Abstract Objectives Many persons with an HIV infection and undergoing treatment still experience weight loss, hyperglycemia, hyperlipidemia, gastrointestinal issues (diarrhea and malabsorption), and symptoms of lipodystrophy. Symptoms include NAFLD and liver fibrosis. The gut microbiota and short chain volatile fatty acids (SCVFA) interface with other body systems. Dysbiosis of the gut microbiota due to pharmaceuticals, malabsorption, and chronic diseases is associated with milieu of imbalances indicated by the modification of the SCVFA profile. This study aimed to further elucidate the relationship between gut microbiota fermentation profiles, serum and fecal long chain fatty acid profiles, NAFLD, liver fibrosis, and anthropometric measures in HIV infected males. Methods This research enrolled 14 HIV-infected and 14 non-infected males that were matched for age and body mass index (BMI). Anthropometric measurements BMI and hip to waist ratio were obtained, along with a liver scan for fatty liver and fibrosis using the ARFI ultrasound technique as well as a single blood draw via venipuncture. A full bowel movement was collected for each participant, a small aliquot was collected for future microbiome analysis, and the remainder was freeze-dried and stored at −80 C. Proximate analysis of fecal fat content was analyzed by soxhlet extraction. Fermentation profile of both fecal SCVFA and LCFA, and serum LCFA were analyzed via gas chromatography. Results Significant differences in levels of specific SCVFAs were found between groups, with male controls having significantly higher amounts of acetate (P < 0.046), butyrate (P < 0.033), and valerate (P < .006). Serum LCFA were similar between groups with a few exceptions. Anthropometric data approached statistical significance, with the HIV infected males exhibiting a greater value for liver damage (P = 0.060) and hip to waist ratio (P = 0.015). Conclusions In addition to identifying altered lipid circulation and liver damage, this research suggests differences in microbial communities between HIV-infected and non-infected individuals. Planned future microbiome analysis will help to correlate bacterial populations with altered fecal fermentation profiles. Funding Sources Seed Grant, Center of Excellence in Inflammation, Infectious Diseases and Immunity, ETSU.

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Gut microbiota signature of pathogen-dependent dysbiosis in viral gastroenteritis

Scientific Reports ◽

10.1038/s41598-021-93345-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Taketoshi Mizutani ◽

Samuel Yaw Aboagye ◽

Aya Ishizaka ◽

Theophillus Afum ◽

Gloria Ivy Mensah ◽

...

Keyword(s):

Species Richness ◽

16S Rrna ◽

Gut Microbiota ◽

Metabolic Pathways ◽

Diversity Analysis ◽

Viral Gastroenteritis ◽

Metabolism Pathway ◽

Microbiome Analysis ◽

Rrna Sequencing ◽

Serious Disease

AbstractAcute gastroenteritis associated with diarrhea is considered a serious disease in Africa and South Asia. In this study, we examined the trends in the causative pathogens of diarrhea and the corresponding gut microbiota in Ghana using microbiome analysis performed on diarrheic stools via 16S rRNA sequencing. In total, 80 patients with diarrhea and 34 healthy adults as controls, from 2017 to 2018, were enrolled in the study. Among the patients with diarrhea, 39 were norovirus-positive and 18 were rotavirus-positive. The analysis of species richness (Chao1) was lower in patients with diarrhea than that in controls. Beta-diversity analysis revealed significant differences between the two groups. Several diarrhea-related pathogens (e.g., Escherichia-Shigella, Klebsiella and Campylobacter) were detected in patients with diarrhea. Furthermore, co-infection with these pathogens and enteroviruses (e.g., norovirus and rotavirus) was observed in several cases. Levels of both Erysipelotrichaceae and Staphylococcaceae family markedly differed between norovirus-positive and -negative diarrheic stools, and the 10 predicted metabolic pathways, including the carbohydrate metabolism pathway, showed significant differences between rotavirus-positive patients with diarrhea and controls. This comparative study of diarrheal pathogens in Ghana revealed specific trends in the gut microbiota signature associated with diarrhea and that pathogen-dependent dysbiosis occurred in viral gastroenteritis.

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