Metataxonomics contributes to unravel the microbiota of a Brazilian dairy

2020 ◽  
Vol 87 (3) ◽  
pp. 360-363
Author(s):  
Diego Araújo Frazilio ◽  
Otávio Guilherme Gonçalves de Almeida ◽  
Carlos Augusto Fernandes de Oliveira ◽  
Sarah Hwa In Lee ◽  
Carlos Humberto Corassin ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Raw Material ◽  
Rrna Gene ◽  
Food Protection ◽  
The Core ◽  
Food Contact ◽  
Food Contact Surfaces ◽  
Contact Surfaces ◽  
Rrna Gene Sequencing

AbstractFor this research communication, 90 samples of a Brazilian dairy were combined into four groups (raw material, final product, food-contact and non-food contact surfaces) and analyzed by metataxonomics based on 16S rRNA gene sequencing. The results showed high alpha-diversity indexes for final product and non-food contact surfaces but, overall, beta-diversity indexes were low. The samples were separated in two main clusters, and the core microbiota was composed by Macrococcus, Alkaliphilus, Vagococcus, Lactobacillus, Marinilactibacillus, Streptococcus, Lysinibacillus, Staphylococcus, Clostridium, Halomonas, Lactococcus, Enterococcus, Bacillus and Psychrobacter. These results highlight that rare taxa occur in dairies, and this may aid the development of strategies for food protection.

scholarly journals Impact of Diabetes on the Gut and Salivary IgA Microbiomes

2020 ◽  
Vol 88 (12) ◽  
Author(s):  
Eric L. Brown ◽  
Heather T. Essigmann ◽  
Kristi L. Hoffman ◽  
Noah W. Palm ◽  
Sarah M. Gunter ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Immunoglobulin A ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Immune Responses ◽  
Mucosal Surfaces ◽  
Immune Mediated ◽  
Rrna Gene Sequencing ◽  
Immune Exclusion

ABSTRACT Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.

scholarly journals Inbreeding Alters the Gut Microbiota of the Banna Minipig

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2125
Author(s):  
Limin Wei ◽  
Bo Zeng ◽  
Siyuan Zhang ◽  
Feng Li ◽  
Fanli Kong ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gene Sequencing ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Isoleucine Metabolism ◽  
Dominant Bacteria ◽  
The Impact ◽  
Predicted Function

The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

scholarly journals Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sebastian von Huth ◽  
Louise Bruun Thingholm ◽  
Corinna Bang ◽  
Malte C. Rühlemann ◽  
Andre Franke ◽  
...  
Keyword(s):  
Room Temperature ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Occult Blood ◽  
Faecal Occult Blood Test ◽  
Rrna Gene ◽  
Long Term Storage ◽  
Fresh Frozen ◽  
Rrna Gene Sequencing ◽  
Filter Papers

AbstractThe gut microbiota is recognized as having major impact in health and disease. Sample storage is an important aspect to obtain reliable results. Mostly recommended is immediate freezing, however, this is not always feasible. Faecal occult blood test (FOBT) papers are an appealing solution in such situations, and most studies find these to be applicable, showing no major changes within 7 days storage at room temperature (RT). As fieldwork often requires RT storage for longer periods, evaluation of this is warranted. We performed 16S rRNA gene sequencing of 19 paired faecal samples immediately frozen or kept five weeks and five months at RT on FOBT papers. Alpha-diversity evaluation revealed no effect of FOBT storage, and evaluation of beta-diversity showed that host explained 65% of community variation, while storage method explained 5%. Evaluation of community dispersion and the Firmicutes/Bacteroidetes ratio revealed a larger effect of storage time for fresh-frozen samples. Single taxa evaluation (order-to-genus level) showed significant alterations of four (of 37) genera after five weeks and five genera after five months. When comparing the two timepoints, alterations were only detectable for fresh-frozen samples. Our findings reveal that long term storage on FOBT papers is an applicable approach for microbiota research.

scholarly journals Longitudinal Characterization of the Tumoral Microbiome during Radiotherapy in HPV-associated Oropharynx Cancer

2020 ◽  
Author(s):  
Houda Bahig ◽  
Clifton D Fuller ◽  
Aparna Mitra ◽  
Travis Solley ◽  
Sweet Ping Ng ◽  
...  
Keyword(s):  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Concurrent Chemotherapy ◽  
Rrna Gene ◽  
Entire Cohort ◽  
Oropharynx Cancer ◽  
History Of ◽  
Rrna Gene Sequencing ◽  
Never Smokers

ABSTRACTPurposeTo describe the baseline and serial tumor microbiome in HPV-associated oropharynx cancer (OPC) over the course of radiotherapy (RT).MethodsPatients with newly diagnosed HPV-associated OPC treated with definitive radiotherapy +/- concurrent chemotherapy were enrolled in this prospective study. Using 16S rRNA gene sequencing, dynamic changes in tumor microbiome during RT were investigated. Surface tumor samples were obtained before RT and at week 1, 3 and 5 of RT. Radiological primary tumor response at mid-treatment was categorized as complete (CR) or partial (PR).ResultsTen patients were enrolled. Mean age was 63 years (range: 51-71). As per AJCC 8th Ed, 50%, 20% and 30% of patients had stage I, II and III, respectively. At 4-weeks, 7 patients had CR and 3 patients had PR; at follow-up imaging post treatment, all patients had CR. Baseline diversity of tumoral and buccal microbiomes was not statistically different. For the entire cohort, alpha diversity was significantly decreased over the course of treatment (p=0.02). There was a significant alteration in the bacterial community within the first week of radiation. Baseline tumor alpha diversity of patients with CR was significantly higher than those with PR (p=0.03). While patients with CR had significant reduction in diversity over the course of radiation (p=0.02), the diversity remained unchanged in patients with PR. Patients with history of smoking had significantly increased abundance of Granulicatella (p=0.04), and Kingella (0.05) and lower abundance of Alloprevotella (p=0.04) compared to never smokers.ConclusionsThe tumor microbiome of HPV-associated OPC exhibits reduced alpha diversity and altered taxa abundance over the course of radiotherapy. The baseline bacterial profiles of smokers vs. non-smokers were inherently different. Baseline tumor alpha diversity of patients with CR was higher than patients with PR, suggesting that the microbiome as a biomarker of radiation response deserves further investigation.

scholarly journals Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population

2021 ◽  
Vol 11 ◽  
Author(s):  
Yi-Jing Jia ◽  
Ying Liao ◽  
Yong-Qiao He ◽  
Mei-Qi Zheng ◽  
Xia-Ting Tong ◽  
...  
Keyword(s):  
Cigarette Smoking ◽  
Chinese Population ◽  
Sugar Metabolism ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Amino Sugar ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Haemophilus Parainfluenzae ◽  
Rrna Gene Sequencing

The oral microbiota has been observed to be influenced by cigarette smoking and linked to several human diseases. However, research on the effect of cigarette smoking on the oral microbiota has not been systematically conducted in the Chinese population. We profiled the oral microbiota of 316 healthy subjects in the Chinese population by 16S rRNA gene sequencing. The alpha diversity of oral microbiota was different between never smokers and smokers (P = 0.002). Several bacterial taxa were first reported to be associated with cigarette smoking by LEfSe analysis, including Moryella (q = 1.56E-04), Bulleidia (q = 1.65E-06), and Moraxella (q = 3.52E-02) at the genus level and Rothia dentocariosa (q = 1.55E-02), Prevotella melaninogenica (q = 8.48E-08), Prevotella pallens (q = 4.13E-03), Bulleidia moorei (q = 1.79E-06), Rothia aeria (q = 3.83E-06), Actinobacillus parahaemolyticus (q = 2.28E-04), and Haemophilus parainfluenzae (q = 4.82E-02) at the species level. Two nitrite-producing bacteria that can increase the acidity of the oral cavity, Actinomyces and Veillonella, were also enriched in smokers with FDR-adjusted q-values of 3.62E-06 and 1.10E-06, respectively. Notably, we observed that two acid production-related pathways, amino acid-related enzymes (q = 6.19E-05) and amino sugar and nucleotide sugar metabolism (q = 2.63E-06), were increased in smokers by PICRUSt analysis. Finally, the co-occurrence analysis demonstrated that smoker-enriched bacteria were significantly positively associated with each other and were negatively correlated with the bacteria decreased in smokers. Our results suggested that cigarette smoking may affect oral health by creating a different environment by altering bacterial abundance, connections among oral microbiota, and the microbiota and their metabolic function.

scholarly journals The bladder microbiome, metabolome, cytokines, and phenotypes in patients with systemic lupus erythematosus

2022 ◽  
Author(s):  
Fengping Liu ◽  
Jingjie Du ◽  
Qixiao Zhai ◽  
Jialin Hu ◽  
Aaron W. Miller ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Complement C3 ◽  
Rrna Gene ◽  
Systemic Lupus ◽  
Disease States ◽  
Metabolomic Profiling ◽  
Rrna Gene Sequencing

Background and aims: Emerging studies reveal a unique bacterial community in the human bladder, with alteration of composition associated to disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease that is characterized by frequent impairment of the kidney. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between microbiome and metabolome, cytokines, and disease profiles. Methods and materials: We recruited a cohort of 50 SLE patients and 50 individually matched asymptomatic controls. We used transurethral catheterization to collect urine samples, 16S rRNA gene sequencing to profile bladder microbiomes, and LC-MS/MS to perform untargeted metabolomic profiling. Results: Compared to controls, SLE patients possessed a unique bladder microbial community and increased alpha diversity. These differences were accompanied by differences in urinary metabolomes, cytokines, and patients’ disease profiles. The SLE-enriched genera, including Bacteroides, were positively correlated with several SLE-enriched metabolites, including olopatadine. The SLE-depleted genera, such as Pseudomonas, were negatively correlated to SLE-depleted cytokines, including IL-8. Alteration of the bladder microbiome was associated with disease profile. For example, the genera Megamonas and Phocaeicola were negatively correlated with serum complement C3, and Streptococcus was positively correlated with IgG. Conclusions: Our present study reveals associations between the bladder microbiome and the urinary metabolome, cytokines, and disease phenotypes. Our results could help identify biomarkers for SLE.

scholarly journals Tongue microbiome of smokeless tobacco users

2020 ◽  
Author(s):  
Esam Halboub ◽  
Mohammed Alakhali ◽  
Abdulwahhab H. Al-Amir ◽  
Husham E. Homeida ◽  
Divyashri Baraniya ◽  
...  
Keyword(s):  
Smokeless Tobacco ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Cross Sectional Study ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Oral Carcinogenesis ◽  
Rothia Mucilaginosa ◽  
Rrna Gene Sequencing

Abstract Background The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This cross sectional study sought to assess the effect of using shammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from twenty-nine shammah users (SU; 27.34±6.9 years) and 23 shammah non-users (SNU; 27.7±7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R. Results A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus , Leptotrichia , Actinomyces , Veillonella , Haemophilus , Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P=0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤ 0.2 and could cluster the two groups separately: Rothia mucilaginosa , Streptococcus sp. oral taxon 66, Actinomyces meyeri , Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU. Conclusion Shammah use induces tongue microbiome changes that may be relevant to oral carcinogenesis, namely enrichment of species with high acetaldehyde production potential, which warrants further investigation.

Microbiological contamination of ready to eat algae and evaluation of Bacillus cereus behavior by microbiological challenge test

2021 ◽  
Author(s):  
Francesco Martelli ◽  
Martina Marrella ◽  
Camilla Lazzi ◽  
Erasmo Neviani ◽  
Valentina Bernini
Keyword(s):  
Bacillus Cereus ◽  
Foodborne Pathogens ◽  
Challenge Test ◽  
Microbiological Quality ◽  
16S Rrna Gene Sequencing ◽  
Raw Material ◽  
Palmaria Palmata ◽  
Rrna Gene ◽  
Related Risk ◽  
Rrna Gene Sequencing

Consumption of seaweeds, often categorized as a superfood, is becoming popular in western countries. Algae can be marketed fresh, but are usually sold dehydrated to ensure longer shelf life. The consumption, often as ready to eat, open up possible risks for public health because of foodborne pathogens that can contaminate the raw material during harvesting or manipulation. In this study, fourteen ready to eat foods based on dehydrated algae, representative of the most consumed species, were considered. The microbial content, with a focus on Listeria monocytogenes and Bacillus cereus, was investigated by plate counts and B. cereus strains were isolated and identified by 16s rRNA gene sequencing. The microbiological quality was heterogeneous among the samples and, in particular, marine bacteria, Listeria spp., B. cereus and coliforms were detected. To contribute to related risk assessment, the ability of B. cereus to grow during refrigerated storage was evaluated, to our knowledge for the first time, by a microbiological challenge test on two ready to eat foods based on Undaria pinnatifida and Palmaria palmata.  Despite this study demonstrating the inability of B. cereus to proliferate in seaweed-based food, its presence in dehydrated foodstuffs cannot rule out the replication after rehydration before consumption, making it necessary to shed light on the possible risks for consumers.

scholarly journals Low Diversity in Nasal Microbiome Associated with Staphylococcus aureus Colonization and Bloodstream Infections in Hospitalized Neonates

2021 ◽  
Author(s):  
Ni Zhao ◽  
Dina F Khamash ◽  
Hyunwook Koh ◽  
Annie Voskertchian ◽  
Emily Egbert ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Alpha Diversity ◽  
Bloodstream Infections ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Case Control Studies ◽  
Wilcoxon Rank Sum Test ◽  
Microbiome Diversity ◽  
Matched Case ◽  
Rrna Gene Sequencing

Abstract Background Staphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Little data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection. Methods We performed two matched case-control studies (colonization cohort – neonates who did and did not acquire S. aureus colonization; bacteremia cohort - neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in two intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge, cultured for S. aureus, and the nasal microbiome characterized using 16S rRNA gene sequencing. Results In the colonization cohort, 43 S. aureus colonized neonates were matched to 82 controls. At first week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank sum test p<0.05) and differed in beta diversity (omnibus MiRKAT p=0.002) even after adjusting for birth weight (p=0.01). The bacteremia cohort included 10 neonates of which 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared to colonized neonates and controls. Conclusions The association of increased S. aureus abundance and decrease of microbiome diversity suggests the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.

scholarly journals Alterations of Thyroid Microbiota Across Different Thyroid Microhabitats in Patients With Thyroid Carcinoma

2021 ◽  
Author(s):  
Daofeng Dai ◽  
Yang Yan ◽  
Yong Yang ◽  
Tianfeng Dang ◽  
Jiansheng Xiao ◽  
...  
Keyword(s):  
Thyroid Carcinoma ◽  
Incidence Rate ◽  
Area Under The Curve ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Core ◽  
Node Metastasis ◽  
Tumor Tissues ◽  
Rrna Gene Sequencing

Abstract Background: In recent years, the incidence rate of Thyroid carcinoma(TC) has been increasing worldwide. Thus, research on factors of TC carcinogenesis may promote TC prevention and decrease the incidence rate. There are several studies targeting the correlation between gut microbiota and thyroid disease. Carcinogenesis of several malignancies is influenced by microbiota. However, thyroid microbiome of TC has not been revealed. This study investigated thyroid microbiota in different TC microhabitats. Methods: We performed 16s rRNA gene sequencing using tumor tissues and matched peritumor tissues from 30 patients with TC to characterize thyroid microbiota. Results: The richness and diversity of thyroid microbiota were lower in TC tumor samples than in matched peritumor tissues. At the genus level, the core microbiota of thyroid included Sphingomonas, Comamonas, Acinetobacter, Pseudomonas, Microvirgula, and Soonwooa. The abundance of Sphingomonas and Aeromonas was significantly increased in tumor tissues, while the abundance of Comamonas, Acinetobacter, and Peptostreptococcus was significantly enhanced in peritumor tissues. The combination of Comamonas and Sphingomonas could discriminate tumor samples from peritumor samples with an area under the curve (AUC) of 0.981 (95% confidence interval [CI]: 0.949-1.000). The abundance of Sphingomonas was significantly higher in N1 stage than in N0 stage. Sphingomonas could distinguish between N0 and N1 stage with an AUC of 0.964 (95% CI: 0.907-1.000).Conclusions: The microbial diversity and composition were significantly different between peritumor and tumor microhabitats from patients with TC, which may eventually affect TC carcinogenesis and progression. The combination of Comamonas and Sphingomonas could serve as a powerful biomarker for discrimination between tumor and peritumor tissues. Furthermore, the higher abundance of Sphingomonas was correlated with lymph node metastasis, indicating that it may play a role in promoting TC progression.

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